diff --git a/hyracks-storage-am-lsm-invertedindex/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/invertedindex/impls/LSMInvertedIndex.java b/hyracks-storage-am-lsm-invertedindex/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/invertedindex/impls/LSMInvertedIndex.java
index 784aa35..ef73413 100644
--- a/hyracks-storage-am-lsm-invertedindex/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/invertedindex/impls/LSMInvertedIndex.java
+++ b/hyracks-storage-am-lsm-invertedindex/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/invertedindex/impls/LSMInvertedIndex.java
@@ -14,6 +14,7 @@
  */
 package edu.uci.ics.hyracks.storage.am.lsm.invertedindex.impls;
 
+import java.io.File;
 import java.util.ArrayList;
 import java.util.LinkedList;
 import java.util.List;
@@ -25,8 +26,10 @@
 import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
 import edu.uci.ics.hyracks.api.io.FileReference;
 import edu.uci.ics.hyracks.dataflow.common.data.accessors.ITupleReference;
+import edu.uci.ics.hyracks.storage.am.btree.frames.BTreeLeafFrameType;
 import edu.uci.ics.hyracks.storage.am.btree.impls.BTree;
 import edu.uci.ics.hyracks.storage.am.btree.impls.RangePredicate;
+import edu.uci.ics.hyracks.storage.am.btree.util.BTreeUtils;
 import edu.uci.ics.hyracks.storage.am.common.api.IIndexAccessor;
 import edu.uci.ics.hyracks.storage.am.common.api.IIndexBulkLoadContext;
 import edu.uci.ics.hyracks.storage.am.common.api.IIndexBulkLoader;
@@ -35,9 +38,11 @@
 import edu.uci.ics.hyracks.storage.am.common.api.IModificationOperationCallback;
 import edu.uci.ics.hyracks.storage.am.common.api.ISearchOperationCallback;
 import edu.uci.ics.hyracks.storage.am.common.api.ISearchPredicate;
+import edu.uci.ics.hyracks.storage.am.common.api.ITreeIndex;
 import edu.uci.ics.hyracks.storage.am.common.api.IndexException;
 import edu.uci.ics.hyracks.storage.am.common.api.IndexType;
 import edu.uci.ics.hyracks.storage.am.common.dataflow.IIndex;
+import edu.uci.ics.hyracks.storage.am.common.impls.NoOpOperationCallback;
 import edu.uci.ics.hyracks.storage.am.common.ophelpers.MultiComparator;
 import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMComponentFinalizer;
 import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMFileManager;
@@ -46,16 +51,21 @@
 import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMIOOperationCallback;
 import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMIOOperationScheduler;
 import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMIndex;
+import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMIndexAccessor;
 import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMMergePolicy;
 import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMOperationTracker;
+import edu.uci.ics.hyracks.storage.am.lsm.common.freepage.InMemoryBufferCache;
 import edu.uci.ics.hyracks.storage.am.lsm.common.freepage.InMemoryFreePageManager;
+import edu.uci.ics.hyracks.storage.am.lsm.common.impls.BTreeFactory;
+import edu.uci.ics.hyracks.storage.am.lsm.common.impls.BlockingIOOperationCallback;
 import edu.uci.ics.hyracks.storage.am.lsm.common.impls.LSMHarness;
 import edu.uci.ics.hyracks.storage.am.lsm.invertedindex.api.IInvertedIndex;
-import edu.uci.ics.hyracks.storage.am.lsm.invertedindex.api.IInvertedListCursor;
-import edu.uci.ics.hyracks.storage.am.lsm.invertedindex.impls.LSMInvertedIndexFileManager.LSMInvertedFileNameComponent;
+import edu.uci.ics.hyracks.storage.am.lsm.invertedindex.impls.LSMInvertedIndexFileManager.LSMRInvertedIndexFileNameComponent;
 import edu.uci.ics.hyracks.storage.am.lsm.invertedindex.inmemory.InMemoryInvertedIndex;
-import edu.uci.ics.hyracks.storage.am.lsm.invertedindex.ondisk.OnDiskInvertedIndexFactory;
 import edu.uci.ics.hyracks.storage.am.lsm.invertedindex.ondisk.OnDiskInvertedIndex;
+import edu.uci.ics.hyracks.storage.am.lsm.invertedindex.ondisk.OnDiskInvertedIndexFactory;
+import edu.uci.ics.hyracks.storage.am.lsm.invertedindex.tokenizers.IBinaryTokenizerFactory;
+import edu.uci.ics.hyracks.storage.am.lsm.invertedindex.util.InvertedIndexUtils;
 import edu.uci.ics.hyracks.storage.common.buffercache.IBufferCache;
 import edu.uci.ics.hyracks.storage.common.file.IFileMapProvider;
 
@@ -63,15 +73,15 @@
 	private final Logger LOGGER = Logger.getLogger(LSMInvertedIndex.class.getName());
 	
 	public class LSMInvertedIndexComponent {
-        private final IIndex invIndex;
+        private final IInvertedIndex invIndex;
         private final BTree deleteKeysBTree;
 
-        LSMInvertedIndexComponent(IIndex invIndex, BTree deleteKeysBTree) {
+        LSMInvertedIndexComponent(IInvertedIndex invIndex, BTree deleteKeysBTree) {
             this.invIndex = invIndex;
             this.deleteKeysBTree = deleteKeysBTree;
         }
 
-        public IIndex getInvIndex() {
+        public IInvertedIndex getInvIndex() {
             return invIndex;
         }
 
@@ -86,11 +96,15 @@
     protected final LSMInvertedIndexComponent memComponent;
     protected final IBufferCache memBufferCache;
     protected final InMemoryFreePageManager memFreePageManager;
-
+    protected final IBinaryTokenizerFactory tokenizerFactory;
+    protected FileReference memDeleteKeysBTreeFile = new FileReference(new File("membtree"));
+    
     // On-disk components.
     protected final ILSMFileManager fileManager;
     // For creating inverted indexes in flush and merge.
     protected final OnDiskInvertedIndexFactory diskInvIndexFactory;
+    // For creating deleted-keys BTrees in flush and merge.
+    protected final BTreeFactory diskBTreeFactory;
     protected final IBufferCache diskBufferCache;
     protected final IFileMapProvider diskFileMapProvider;
     // List of LSMInvertedIndexComponent instances. Using Object for better sharing via
@@ -107,92 +121,210 @@
     
     private boolean isActivated = false;
 
-    public LSMInvertedIndex(IBufferCache memBufferCache, InMemoryFreePageManager memFreePageManager, OnDiskInvertedIndexFactory diskInvIndexFactory,
-            ILSMFileManager fileManager, IFileMapProvider diskFileMapProvider, ITypeTraits[] invListTypeTraits,
+    public LSMInvertedIndex(IBufferCache memBufferCache, InMemoryFreePageManager memFreePageManager,
+            OnDiskInvertedIndexFactory diskInvIndexFactory, BTreeFactory diskBTreeFactory, ILSMFileManager fileManager,
+            IFileMapProvider diskFileMapProvider, ITypeTraits[] invListTypeTraits,
             IBinaryComparatorFactory[] invListCmpFactories, ITypeTraits[] tokenTypeTraits,
-            IBinaryComparatorFactory[] tokenCmpFactories, ILSMFlushController flushController,
-            ILSMMergePolicy mergePolicy, ILSMOperationTracker opTracker, ILSMIOOperationScheduler ioScheduler) {
-        // TODO: Finish this one properly.
-        InMemoryInvertedIndex memInvIndex = null;
-        BTree deleteKeysBTree = null;
+            IBinaryComparatorFactory[] tokenCmpFactories, IBinaryTokenizerFactory tokenizerFactory,
+            ILSMFlushController flushController, ILSMMergePolicy mergePolicy, ILSMOperationTracker opTracker,
+            ILSMIOOperationScheduler ioScheduler) throws IndexException {
+        InMemoryInvertedIndex memInvIndex = InvertedIndexUtils.createInMemoryBTreeInvertedindex(memBufferCache,
+                memFreePageManager, invListTypeTraits, invListCmpFactories, tokenTypeTraits, tokenCmpFactories,
+                tokenizerFactory);
+        BTree deleteKeysBTree = BTreeUtils.createBTree(memBufferCache, diskFileMapProvider, invListTypeTraits,
+                invListCmpFactories, BTreeLeafFrameType.REGULAR_NSM, memDeleteKeysBTreeFile);
         memComponent = new LSMInvertedIndexComponent(memInvIndex, deleteKeysBTree);
         this.memBufferCache = memBufferCache;
         this.memFreePageManager = memFreePageManager;
+        this.tokenizerFactory = tokenizerFactory;
         this.fileManager = fileManager;
-        this.diskInvIndexFactory = diskInvIndexFactory;        
+        this.diskInvIndexFactory = diskInvIndexFactory;
+        this.diskBTreeFactory = diskBTreeFactory;
         this.diskBufferCache = diskInvIndexFactory.getBufferCache();
         this.diskFileMapProvider = diskFileMapProvider;
         this.invListTypeTraits = invListTypeTraits;
         this.invListCmpFactories = invListCmpFactories;
         this.tokenTypeTraits = tokenTypeTraits;
         this.tokenCmpFactories = tokenCmpFactories;
-        
         this.lsmHarness = new LSMHarness(this, flushController, mergePolicy, opTracker, ioScheduler);
         this.componentFinalizer = new InvertedIndexComponentFinalizer(diskFileMapProvider);
     }
 
     @Override
-    public synchronized void create(int indexFileId) throws HyracksDataException {
+    public synchronized void create() throws HyracksDataException {
         if (isActivated) {
-            return;
+            throw new HyracksDataException("Failed to create the index since it is activated.");
         }
-        
-        // TODO: What else is needed here?
-        memoryInvertedIndex.create(indexFileId);
+
+        fileManager.deleteDirs();
         fileManager.createDirs();
     }
 
     @Override
-    public void open(int indexFileId) throws HyracksDataException {
-        synchronized (this) {
-            if (isOpen)
-                return;
-
-            isOpen = true;
-            memoryInvertedIndex.open(indexFileId);
-            // TODO: What else is needed here?
-            // ...
+    // TODO: Properly implement this one.
+    public synchronized void activate() throws HyracksDataException {
+        if (isActivated) {
+            return;
         }
 
+        ((InMemoryBufferCache) memComponent.getInvIndex().getBufferCache()).open();
+        memComponent.getInvIndex().create();
+        memComponent.getDeletedKeysBTree().create();
+        List<Object> validFileNames = fileManager.cleanupAndGetValidFiles(componentFinalizer);
+        for (Object o : validFileNames) {
+            LSMRInvertedIndexFileNameComponent component = (LSMRInvertedIndexFileNameComponent) o;
+            FileReference rtreeFile = new FileReference(new File(component.getRTreeFileName()));
+            FileReference btreeFile = new FileReference(new File(component.getBTreeFileName()));
+            RTree rtree = (RTree) createDiskTree(diskRTreeFactory, rtreeFile, false);
+            BTree btree = (BTree) createDiskTree(diskBTreeFactory, btreeFile, false);
+            LSMRTreeComponent diskComponent = new LSMRTreeComponent(rtree, btree);
+            diskComponents.add(diskComponent);
+        }
+        isActivated = true;
+    }
+
+    protected IInvertedIndex createDiskInvIndex(OnDiskInvertedIndexFactory invIndexFactory, FileReference fileRef, boolean create) throws HyracksDataException, IndexException {
+        IInvertedIndex invIndex = invIndexFactory.createIndexInstance(fileRef);
+        if (create) {
+            invIndex.create();
+        }
+        // Will be closed during cleanup of merge().
+        invIndex.activate();
+        return invIndex;
+    }
+    
+    protected ITreeIndex createDiskDeletedKeysBTree(BTreeFactory btreeFactory, FileReference fileRef, boolean create) throws HyracksDataException, IndexException {
+        ITreeIndex btree = btreeFactory.createIndexInstance(fileRef);
+        if (create) {
+            btree.create();
+        }
+        // Will be closed during cleanup of merge().
+        btree.activate();
+        return btree;
+    }
+    
+    @Override
+    public void clear() throws HyracksDataException {
+        if (!isActivated) {
+            throw new HyracksDataException("Failed to clear the index since it is not activated.");
+        }
+        memComponent.getInvIndex().clear();
+        memComponent.getDeletedKeysBTree().clear();
+        for (Object o : diskComponents) {
+            LSMInvertedIndexComponent component = (LSMInvertedIndexComponent) o;
+            component.getInvIndex().deactivate();
+            component.getDeletedKeysBTree().deactivate();
+            component.getInvIndex().destroy();
+            component.getDeletedKeysBTree().destroy();
+        }
+        diskComponents.clear();
     }
 
     @Override
-    public void close() throws HyracksDataException {
-        synchronized (this) {
-            if (!isOpen) {
-                return;
-            }
-            // TODO: What else is needed here?
-            // ...
-            memoryInvertedIndex.close();
-            isOpen = false;
+    public synchronized void deactivate() throws HyracksDataException {
+        if (!isActivated) {
+            return;
         }
+
+        isActivated = false;
+
+        BlockingIOOperationCallback blockingCallBack = new BlockingIOOperationCallback();
+        ILSMIndexAccessor accessor = (ILSMIndexAccessor) createAccessor(NoOpOperationCallback.INSTANCE,
+                NoOpOperationCallback.INSTANCE);
+        lsmHarness.getIOScheduler().scheduleOperation(accessor.createFlushOperation(blockingCallBack));
+        try {
+            blockingCallBack.waitForIO();
+        } catch (InterruptedException e) {
+            throw new HyracksDataException(e);
+        }
+
+        memComponent.getInvIndex().deactivate();
+        memComponent.getDeletedKeysBTree().deactivate();
+        memComponent.getInvIndex().destroy();
+        memComponent.getDeletedKeysBTree().destroy();
+        ((InMemoryBufferCache) memComponent.getInvIndex().getBufferCache()).close();
     }
 
-    public IIndexAccessor createAccessor() {
+    @Override
+    public synchronized void destroy() throws HyracksDataException {
+        if (isActivated) {
+            throw new HyracksDataException("Failed to destroy the index since it is activated.");
+        }
+
+        memComponent.getInvIndex().destroy();
+        memComponent.getDeletedKeysBTree().destroy();        
+        for (Object o : diskComponents) {
+            LSMInvertedIndexComponent component = (LSMInvertedIndexComponent) o;
+            component.getInvIndex().destroy();
+            component.getDeletedKeysBTree().destroy();
+        }
+        fileManager.deleteDirs();
+    }
+
+    @Override
+    public IIndexAccessor createAccessor(IModificationOperationCallback modificationCallback,
+            ISearchOperationCallback searchCallback) {
+        // TODO: Ignore opcallbacks for now.
         return new LSMInvertedIndexAccessor(lsmHarness, createOpContext());
     }
 
-    private LSMInvertedIndexOpContext createOpContext() {
-        return new LSMInvertedIndexOpContext(memoryInvertedIndex);
+    @Override
+    public void validate() throws HyracksDataException {
+        // TODO Auto-generated method stub
+        
     }
 
     @Override
-    public IIndexBulkLoadContext beginBulkLoad(float fillFactor) throws IndexException, HyracksDataException {
+    public long getInMemorySize() {
+        // TODO Auto-generated method stub
+        return 0;
+    }
+
+    @Override
+    public IIndexBulkLoader createBulkLoader(float fillFactor, boolean verifyInput) throws IndexException {
         // TODO Auto-generated method stub
         return null;
     }
 
     @Override
-    public void bulkLoadAddTuple(ITupleReference tuple, IIndexBulkLoadContext ictx) throws HyracksDataException {
+    public ILSMIOOperation createMergeOperation(ILSMIOOperationCallback callback) throws HyracksDataException {
         // TODO Auto-generated method stub
-
+        return null;
     }
 
     @Override
-    public void endBulkLoad(IIndexBulkLoadContext ictx) throws HyracksDataException {
+    public Object merge(List<Object> mergedComponents, ILSMIOOperation operation) throws HyracksDataException,
+            IndexException {
         // TODO Auto-generated method stub
+        return null;
+    }
 
+    @Override
+    public Object flush(ILSMIOOperation operation) throws HyracksDataException, IndexException {
+        // TODO Auto-generated method stub
+        return null;
+    }
+
+    @Override
+    public ILSMFlushController getFlushController() {
+        // TODO Auto-generated method stub
+        return null;
+    }
+
+    @Override
+    public ILSMOperationTracker getOperationTracker() {
+        // TODO Auto-generated method stub
+        return null;
+    }
+
+    @Override
+    public ILSMIOOperationScheduler getIOScheduler() {
+        // TODO Auto-generated method stub
+        return null;
+    }
+
+    private LSMInvertedIndexOpContext createOpContext() {
+        return new LSMInvertedIndexOpContext(memoryInvertedIndex);
     }
 
     @Override
@@ -211,7 +343,6 @@
         // are also supported.
         LSMInvertedIndexOpContext ctx = (LSMInvertedIndexOpContext) ictx;
         memAccessor.insert(tuple);
-
         return true;
     }
 
@@ -315,8 +446,8 @@
 
     @Override
     public void addMergedComponent(Object newComponent, List<Object> mergedComponents) {
-        diskInvertedIndexList.removeAll(mergedComponents);
-        diskInvertedIndexList.addLast(newComponent);
+        diskComponents.removeAll(mergedComponents);
+        diskComponents.addLast(newComponent);
     }
 
     @Override
@@ -457,127 +588,11 @@
 
     @Override
     public List<Object> getDiskComponents() {
-        return diskInvertedIndexList;
+        return diskComponents;
     }
 
     @Override
     public ILSMComponentFinalizer getComponentFinalizer() {
         return componentFinalizer;
     }
-
-    @Override
-    public IInvertedListCursor createInvertedListCursor() {
-        // TODO Auto-generated method stub
-        return null;
-    }
-
-    @Override
-    public void openInvertedListCursor(IInvertedListCursor listCursor, ITupleReference tupleReference)
-            throws HyracksDataException, IndexException {
-        // TODO Auto-generated method stub
-        
-    }
-
-    @Override
-    public IBinaryComparatorFactory[] getInvListElementCmpFactories() {
-        return memoryInvertedIndex.getInvListCmpFactories();
-    }
-
-    @Override
-    public ITypeTraits[] getTypeTraits() {
-        return memoryInvertedIndex.getInvListTypeTraits();
-    }
-
-    @Override
-    public void create() throws HyracksDataException {
-        // TODO Auto-generated method stub
-        
-    }
-
-    @Override
-    public void activate() throws HyracksDataException {
-        // TODO Auto-generated method stub
-        
-    }
-
-    @Override
-    public void clear() throws HyracksDataException {
-        // TODO Auto-generated method stub
-        
-    }
-
-    @Override
-    public void deactivate() throws HyracksDataException {
-        // TODO Auto-generated method stub
-        
-    }
-
-    @Override
-    public void destroy() throws HyracksDataException {
-        // TODO Auto-generated method stub
-        
-    }
-
-    @Override
-    public IIndexAccessor createAccessor(IModificationOperationCallback modificationCallback,
-            ISearchOperationCallback searchCallback) {
-        // TODO Auto-generated method stub
-        return null;
-    }
-
-    @Override
-    public void validate() throws HyracksDataException {
-        // TODO Auto-generated method stub
-        
-    }
-
-    @Override
-    public long getInMemorySize() {
-        // TODO Auto-generated method stub
-        return 0;
-    }
-
-    @Override
-    public IIndexBulkLoader createBulkLoader(float fillFactor, boolean verifyInput) throws IndexException {
-        // TODO Auto-generated method stub
-        return null;
-    }
-
-    @Override
-    public ILSMIOOperation createMergeOperation(ILSMIOOperationCallback callback) throws HyracksDataException {
-        // TODO Auto-generated method stub
-        return null;
-    }
-
-    @Override
-    public Object merge(List<Object> mergedComponents, ILSMIOOperation operation) throws HyracksDataException,
-            IndexException {
-        // TODO Auto-generated method stub
-        return null;
-    }
-
-    @Override
-    public Object flush(ILSMIOOperation operation) throws HyracksDataException, IndexException {
-        // TODO Auto-generated method stub
-        return null;
-    }
-
-    @Override
-    public ILSMFlushController getFlushController() {
-        // TODO Auto-generated method stub
-        return null;
-    }
-
-    @Override
-    public ILSMOperationTracker getOperationTracker() {
-        // TODO Auto-generated method stub
-        return null;
-    }
-
-    @Override
-    public ILSMIOOperationScheduler getIOScheduler() {
-        // TODO Auto-generated method stub
-        return null;
-    }
-
 }
diff --git a/hyracks-storage-am-lsm-invertedindex/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/invertedindex/impls/LSMInvertedIndexFileManager.java b/hyracks-storage-am-lsm-invertedindex/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/invertedindex/impls/LSMInvertedIndexFileManager.java
index 4c893a9..213f87d 100644
--- a/hyracks-storage-am-lsm-invertedindex/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/invertedindex/impls/LSMInvertedIndexFileManager.java
+++ b/hyracks-storage-am-lsm-invertedindex/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/invertedindex/impls/LSMInvertedIndexFileManager.java
@@ -17,37 +17,53 @@
 
 import java.io.File;
 import java.io.FilenameFilter;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
 
 import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
-import edu.uci.ics.hyracks.control.nc.io.IOManager;
+import edu.uci.ics.hyracks.api.io.FileReference;
+import edu.uci.ics.hyracks.api.io.IIOManager;
+import edu.uci.ics.hyracks.api.io.IODeviceHandle;
+import edu.uci.ics.hyracks.storage.am.common.api.ITreeIndex;
+import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMComponentFinalizer;
 import edu.uci.ics.hyracks.storage.am.lsm.common.impls.LSMTreeFileManager;
+import edu.uci.ics.hyracks.storage.am.lsm.common.impls.TreeIndexFactory;
 import edu.uci.ics.hyracks.storage.common.file.IFileMapProvider;
 
+// TODO: Implement this one properly!
 public class LSMInvertedIndexFileManager extends LSMTreeFileManager {
-
-    private static final String INVERTED_STRING = "i";
+    private static final String RTREE_STRING = "r";
     private static final String BTREE_STRING = "b";
 
+    private final TreeIndexFactory<? extends ITreeIndex> rtreeFactory;
+    private final TreeIndexFactory<? extends ITreeIndex> btreeFactory;
+
     private static FilenameFilter btreeFilter = new FilenameFilter() {
         public boolean accept(File dir, String name) {
             return !name.startsWith(".") && name.endsWith(BTREE_STRING);
         }
     };
-    
-    private static FilenameFilter invertedFilter = new FilenameFilter() {
+
+    private static FilenameFilter rtreeFilter = new FilenameFilter() {
         public boolean accept(File dir, String name) {
-            return !name.startsWith(".") && name.endsWith(INVERTED_STRING);
+            return !name.startsWith(".") && name.endsWith(RTREE_STRING);
         }
     };
-    
-    public LSMInvertedIndexFileManager(IOManager ioManager, IFileMapProvider fileMapProvider, String baseDir) {
-        super(ioManager, fileMapProvider, baseDir);
+
+    public LSMInvertedIndexFileManager(IIOManager ioManager, IFileMapProvider fileMapProvider, FileReference file,
+            TreeIndexFactory<? extends ITreeIndex> rtreeFactory, TreeIndexFactory<? extends ITreeIndex> btreeFactory) {
+        super(ioManager, fileMapProvider, file, null);
+        this.rtreeFactory = rtreeFactory;
+        this.btreeFactory = btreeFactory;
     }
 
     @Override
     public Object getRelFlushFileName() {
         String baseName = (String) super.getRelFlushFileName();
-        return new LSMInvertedFileNameComponent(baseName + SPLIT_STRING + INVERTED_STRING, baseName + SPLIT_STRING
+        return new LSMRInvertedIndexFileNameComponent(baseName + SPLIT_STRING + RTREE_STRING, baseName + SPLIT_STRING
                 + BTREE_STRING);
 
     }
@@ -55,127 +71,125 @@
     @Override
     public Object getRelMergeFileName(String firstFileName, String lastFileName) throws HyracksDataException {
         String baseName = (String) super.getRelMergeFileName(firstFileName, lastFileName);
-        return new LSMInvertedFileNameComponent(baseName + SPLIT_STRING + INVERTED_STRING, baseName + SPLIT_STRING
+        return new LSMRInvertedIndexFileNameComponent(baseName + SPLIT_STRING + RTREE_STRING, baseName + SPLIT_STRING
                 + BTREE_STRING);
     }
 
-//    @Override
-//    public List<Object> cleanupAndGetValidFiles(Object lsmComponent, ILSMComponentFinalizer componentFinalizer) throws HyracksDataException {
-//        List<Object> validFiles = new ArrayList<Object>();
-//        ArrayList<ComparableFileName> allInvertedFiles = new ArrayList<ComparableFileName>();
-//        ArrayList<ComparableFileName> allBTreeFiles = new ArrayList<ComparableFileName>();
-//        LSMInvertedComponent component = (LSMInvertedComponent) lsmComponent;
-//        
-//        // Gather files from all IODeviceHandles.
-//        for (IODeviceHandle dev : ioManager.getIODevices()) {            
-//            getValidFiles(dev, btreeFilter, component.getBTree(), componentFinalizer, allBTreeFiles);
-//            HashSet<String> btreeFilesSet = new HashSet<String>();
-//            for (ComparableFileName cmpFileName : allBTreeFiles) {
-//                int index = cmpFileName.fileName.lastIndexOf(SPLIT_STRING);
-//                btreeFilesSet.add(cmpFileName.fileName.substring(0, index));
-//            }
-//            // List of valid Inverted files that may or may not have a BTree buddy. Will check for buddies below.
-//            ArrayList<ComparableFileName> tmpAllInvertedFiles = new ArrayList<ComparableFileName>();
-//            getValidFiles(dev, invertedFilter, component.getInverted(), componentFinalizer, tmpAllInvertedFiles);
-//            // Look for buddy BTrees for all valid Inverteds. 
-//            // If no buddy is found, delete the file, otherwise add the Inverted to allInvertedFiles. 
-//            for (ComparableFileName cmpFileName : tmpAllInvertedFiles) {
-//                int index = cmpFileName.fileName.lastIndexOf(SPLIT_STRING);
-//                String file = cmpFileName.fileName.substring(0, index);
-//                if (btreeFilesSet.contains(file)) {
-//                    allInvertedFiles.add(cmpFileName);
-//                } else {
-//                    // Couldn't find the corresponding BTree file; thus, delete
-//                    // the Inverted file.
-//                    File invalidInvertedFile = new File(cmpFileName.fullPath);
-//                    invalidInvertedFile.delete();
-//                }
-//            }
-//        }
-//        // Sanity check.
-//        if (allInvertedFiles.size() != allBTreeFiles.size()) {
-//            throw new HyracksDataException("Unequal number of valid Inverted and BTree files found. Aborting cleanup.");
-//        }
-//        
-//        // Trivial cases.
-//        if (allInvertedFiles.isEmpty() || allBTreeFiles.isEmpty()) {
-//            return validFiles;
-//        }
-//
-//        if (allInvertedFiles.size() == 1 && allBTreeFiles.size() == 1) {
-//            validFiles.add(new LSMInvertedFileNameComponent(allInvertedFiles.get(0).fullPath, allBTreeFiles.get(0).fullPath));
-//            return validFiles;
-//        }
-//
-//        // Sorts files names from earliest to latest timestamp.
-//        Collections.sort(allInvertedFiles);
-//        Collections.sort(allBTreeFiles);
-//
-//        List<ComparableFileName> validComparableInvertedFiles = new ArrayList<ComparableFileName>();
-//        ComparableFileName lastInverted = allInvertedFiles.get(0);
-//        validComparableInvertedFiles.add(lastInverted);
-//
-//        List<ComparableFileName> validComparableBTreeFiles = new ArrayList<ComparableFileName>();
-//        ComparableFileName lastBTree = allBTreeFiles.get(0);
-//        validComparableBTreeFiles.add(lastBTree);
-//
-//        for (int i = 1; i < allInvertedFiles.size(); i++) {
-//            ComparableFileName currentInverted = allInvertedFiles.get(i);
-//            ComparableFileName currentBTree = allBTreeFiles.get(i);
-//            // Current start timestamp is greater than last stop timestamp.
-//            if (currentInverted.interval[0].compareTo(lastInverted.interval[1]) > 0
-//                    && currentBTree.interval[0].compareTo(lastBTree.interval[1]) > 0) {
-//                validComparableInvertedFiles.add(currentInverted);
-//                validComparableBTreeFiles.add(currentBTree);
-//                lastInverted = currentInverted;
-//                lastBTree = currentBTree;
-//            } else if (currentInverted.interval[0].compareTo(lastInverted.interval[0]) >= 0
-//                    && currentInverted.interval[1].compareTo(lastInverted.interval[1]) <= 0
-//                    && currentBTree.interval[0].compareTo(lastBTree.interval[0]) >= 0
-//                    && currentBTree.interval[1].compareTo(lastBTree.interval[1]) <= 0) {
-//                // Invalid files are completely contained in last interval.
-//                File invalidInvertedFile = new File(currentInverted.fullPath);
-//                invalidInvertedFile.delete();
-//                File invalidBTreeFile = new File(currentBTree.fullPath);
-//                invalidBTreeFile.delete();
-//            } else {
-//                // This scenario should not be possible.
-//                throw new HyracksDataException("Found LSM files with overlapping but not contained timetamp intervals.");
-//            }
-//        }
-//
-//        // Sort valid files in reverse lexicographical order, such that newer
-//        // files come first.
-//        Collections.sort(validComparableInvertedFiles, recencyCmp);
-//        Collections.sort(validComparableBTreeFiles, recencyCmp);
-//
-//        Iterator<ComparableFileName> invertedFileIter = validComparableInvertedFiles.iterator();
-//        Iterator<ComparableFileName> btreeFileIter = validComparableBTreeFiles.iterator();
-//        while (invertedFileIter.hasNext() && btreeFileIter.hasNext()) {
-//            ComparableFileName cmpInvertedFileName = invertedFileIter.next();
-//            ComparableFileName cmpBTreeFileName = btreeFileIter.next();
-//            validFiles.add(new LSMInvertedFileNameComponent(cmpInvertedFileName.fullPath, cmpBTreeFileName.fullPath));
-//        }
-//
-//        return validFiles;
-//    }
+    @Override
+    public List<Object> cleanupAndGetValidFiles(ILSMComponentFinalizer componentFinalizer) throws HyracksDataException {
+        List<Object> validFiles = new ArrayList<Object>();
+        ArrayList<ComparableFileName> allRTreeFiles = new ArrayList<ComparableFileName>();
+        ArrayList<ComparableFileName> allBTreeFiles = new ArrayList<ComparableFileName>();
 
-    public class LSMInvertedFileNameComponent {
-        private final String invertedFileName;
+        // Gather files from all IODeviceHandles.
+        for (IODeviceHandle dev : ioManager.getIODevices()) {
+            cleanupAndGetValidFilesInternal(dev, btreeFilter, btreeFactory, componentFinalizer, allBTreeFiles);
+            HashSet<String> btreeFilesSet = new HashSet<String>();
+            for (ComparableFileName cmpFileName : allBTreeFiles) {
+                int index = cmpFileName.fileName.lastIndexOf(SPLIT_STRING);
+                btreeFilesSet.add(cmpFileName.fileName.substring(0, index));
+            }
+            // List of valid RTree files that may or may not have a BTree buddy. Will check for buddies below.
+            ArrayList<ComparableFileName> tmpAllRTreeFiles = new ArrayList<ComparableFileName>();
+            cleanupAndGetValidFilesInternal(dev, rtreeFilter, rtreeFactory, componentFinalizer, tmpAllRTreeFiles);
+            // Look for buddy BTrees for all valid RTrees. 
+            // If no buddy is found, delete the file, otherwise add the RTree to allRTreeFiles. 
+            for (ComparableFileName cmpFileName : tmpAllRTreeFiles) {
+                int index = cmpFileName.fileName.lastIndexOf(SPLIT_STRING);
+                String file = cmpFileName.fileName.substring(0, index);
+                if (btreeFilesSet.contains(file)) {
+                    allRTreeFiles.add(cmpFileName);
+                } else {
+                    // Couldn't find the corresponding BTree file; thus, delete
+                    // the RTree file.
+                    File invalidRTreeFile = new File(cmpFileName.fullPath);
+                    invalidRTreeFile.delete();
+                }
+            }
+        }
+        // Sanity check.
+        if (allRTreeFiles.size() != allBTreeFiles.size()) {
+            throw new HyracksDataException("Unequal number of valid RTree and BTree files found. Aborting cleanup.");
+        }
+
+        // Trivial cases.
+        if (allRTreeFiles.isEmpty() || allBTreeFiles.isEmpty()) {
+            return validFiles;
+        }
+
+        if (allRTreeFiles.size() == 1 && allBTreeFiles.size() == 1) {
+            validFiles.add(new LSMRInvertedIndexFileNameComponent(allRTreeFiles.get(0).fullPath, allBTreeFiles.get(0).fullPath));
+            return validFiles;
+        }
+
+        // Sorts files names from earliest to latest timestamp.
+        Collections.sort(allRTreeFiles);
+        Collections.sort(allBTreeFiles);
+
+        List<ComparableFileName> validComparableRTreeFiles = new ArrayList<ComparableFileName>();
+        ComparableFileName lastRTree = allRTreeFiles.get(0);
+        validComparableRTreeFiles.add(lastRTree);
+
+        List<ComparableFileName> validComparableBTreeFiles = new ArrayList<ComparableFileName>();
+        ComparableFileName lastBTree = allBTreeFiles.get(0);
+        validComparableBTreeFiles.add(lastBTree);
+
+        for (int i = 1; i < allRTreeFiles.size(); i++) {
+            ComparableFileName currentRTree = allRTreeFiles.get(i);
+            ComparableFileName currentBTree = allBTreeFiles.get(i);
+            // Current start timestamp is greater than last stop timestamp.
+            if (currentRTree.interval[0].compareTo(lastRTree.interval[1]) > 0
+                    && currentBTree.interval[0].compareTo(lastBTree.interval[1]) > 0) {
+                validComparableRTreeFiles.add(currentRTree);
+                validComparableBTreeFiles.add(currentBTree);
+                lastRTree = currentRTree;
+                lastBTree = currentBTree;
+            } else if (currentRTree.interval[0].compareTo(lastRTree.interval[0]) >= 0
+                    && currentRTree.interval[1].compareTo(lastRTree.interval[1]) <= 0
+                    && currentBTree.interval[0].compareTo(lastBTree.interval[0]) >= 0
+                    && currentBTree.interval[1].compareTo(lastBTree.interval[1]) <= 0) {
+                // Invalid files are completely contained in last interval.
+                File invalidRTreeFile = new File(currentRTree.fullPath);
+                invalidRTreeFile.delete();
+                File invalidBTreeFile = new File(currentBTree.fullPath);
+                invalidBTreeFile.delete();
+            } else {
+                // This scenario should not be possible.
+                throw new HyracksDataException("Found LSM files with overlapping but not contained timetamp intervals.");
+            }
+        }
+
+        // Sort valid files in reverse lexicographical order, such that newer
+        // files come first.
+        Collections.sort(validComparableRTreeFiles, recencyCmp);
+        Collections.sort(validComparableBTreeFiles, recencyCmp);
+
+        Iterator<ComparableFileName> rtreeFileIter = validComparableRTreeFiles.iterator();
+        Iterator<ComparableFileName> btreeFileIter = validComparableBTreeFiles.iterator();
+        while (rtreeFileIter.hasNext() && btreeFileIter.hasNext()) {
+            ComparableFileName cmpRTreeFileName = rtreeFileIter.next();
+            ComparableFileName cmpBTreeFileName = btreeFileIter.next();
+            validFiles.add(new LSMRInvertedIndexFileNameComponent(cmpRTreeFileName.fullPath, cmpBTreeFileName.fullPath));
+        }
+
+        return validFiles;
+    }
+
+    public class LSMRInvertedIndexFileNameComponent {
+        private final String rtreeFileName;
         private final String btreeFileName;
 
-        LSMInvertedFileNameComponent(String invertedFileName, String btreeFileName) {
-            this.invertedFileName = invertedFileName;
+        LSMRInvertedIndexFileNameComponent(String rtreeFileName, String btreeFileName) {
+            this.rtreeFileName = rtreeFileName;
             this.btreeFileName = btreeFileName;
         }
 
-        public String getInvertedFileName() {
-            return invertedFileName;
+        public String getRTreeFileName() {
+            return rtreeFileName;
         }
 
         public String getBTreeFileName() {
             return btreeFileName;
         }
     }
-
 }
diff --git a/hyracks-storage-am-lsm-invertedindex/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/invertedindex/ondisk/OnDiskInvertedIndexFactory.java b/hyracks-storage-am-lsm-invertedindex/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/invertedindex/ondisk/OnDiskInvertedIndexFactory.java
index 306695d..bd2605c 100644
--- a/hyracks-storage-am-lsm-invertedindex/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/invertedindex/ondisk/OnDiskInvertedIndexFactory.java
+++ b/hyracks-storage-am-lsm-invertedindex/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/invertedindex/ondisk/OnDiskInvertedIndexFactory.java
@@ -20,13 +20,13 @@
 import edu.uci.ics.hyracks.api.dataflow.value.ITypeTraits;
 import edu.uci.ics.hyracks.api.io.FileReference;
 import edu.uci.ics.hyracks.storage.am.common.api.IndexException;
-import edu.uci.ics.hyracks.storage.am.common.dataflow.IIndex;
 import edu.uci.ics.hyracks.storage.am.lsm.common.impls.IndexFactory;
+import edu.uci.ics.hyracks.storage.am.lsm.invertedindex.api.IInvertedIndex;
 import edu.uci.ics.hyracks.storage.am.lsm.invertedindex.api.IInvertedListBuilder;
 import edu.uci.ics.hyracks.storage.common.buffercache.IBufferCache;
 import edu.uci.ics.hyracks.storage.common.file.IFileMapProvider;
 
-public class OnDiskInvertedIndexFactory extends IndexFactory<IIndex> {
+public class OnDiskInvertedIndexFactory extends IndexFactory<IInvertedIndex> {
 
     protected final IInvertedListBuilder invListBuilder;
     protected final ITypeTraits[] invListTypeTraits;
@@ -47,7 +47,7 @@
     }
 
     @Override
-    public IIndex createIndexInstance(FileReference file) throws IndexException {
+    public IInvertedIndex createIndexInstance(FileReference file) throws IndexException {
         FileReference btreeFile = new FileReference(new File(file.getFile().getPath() + "_btree"));
         return new OnDiskInvertedIndex(bufferCache, fileMapProvider, invListBuilder, invListTypeTraits, invListCmpFactories,
                 tokenTypeTraits, tokenCmpFactories, btreeFile, file);