diff --git a/hyracks-storage-am-lsm-btree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/btree/impls/LSMBTree.java b/hyracks-storage-am-lsm-btree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/btree/impls/LSMBTree.java
index 6cbc9d7..7850f3d 100644
--- a/hyracks-storage-am-lsm-btree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/btree/impls/LSMBTree.java
+++ b/hyracks-storage-am-lsm-btree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/btree/impls/LSMBTree.java
@@ -49,13 +49,13 @@
 import edu.uci.ics.hyracks.storage.am.common.ophelpers.MultiComparator;
 import edu.uci.ics.hyracks.storage.am.lsm.btree.tuples.LSMBTreeTupleReference;
 import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMComponentFinalizer;
-import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMIndexFileManager;
 import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMFlushController;
 import edu.uci.ics.hyracks.storage.am.lsm.common.api.ILSMIOOperation;
 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.ILSMIndexFileManager;
 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;
@@ -65,8 +65,8 @@
 import edu.uci.ics.hyracks.storage.am.lsm.common.impls.LSMHarness;
 import edu.uci.ics.hyracks.storage.am.lsm.common.impls.LSMMergeOperation;
 import edu.uci.ics.hyracks.storage.am.lsm.common.impls.LSMTreeIndexAccessor;
-import edu.uci.ics.hyracks.storage.am.lsm.common.impls.TreeIndexFactory;
 import edu.uci.ics.hyracks.storage.am.lsm.common.impls.TreeIndexComponentFinalizer;
+import edu.uci.ics.hyracks.storage.am.lsm.common.impls.TreeIndexFactory;
 import edu.uci.ics.hyracks.storage.common.buffercache.IBufferCache;
 import edu.uci.ics.hyracks.storage.common.file.IFileMapProvider;
 
@@ -134,6 +134,7 @@
 
         fileManager.deleteDirs();
         fileManager.createDirs();
+        diskBTrees.clear();
     }
 
     @Override
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 c10c01e..6a2a9b7 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
@@ -163,6 +163,7 @@
 
         fileManager.deleteDirs();
         fileManager.createDirs();
+        diskComponents.clear();
     }
 
     @Override
diff --git a/hyracks-storage-am-lsm-rtree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/rtree/impls/AbstractLSMRTree.java b/hyracks-storage-am-lsm-rtree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/rtree/impls/AbstractLSMRTree.java
index b39d337..d405e39 100644
--- a/hyracks-storage-am-lsm-rtree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/rtree/impls/AbstractLSMRTree.java
+++ b/hyracks-storage-am-lsm-rtree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/rtree/impls/AbstractLSMRTree.java
@@ -120,11 +120,12 @@
     public AbstractLSMRTree(IBufferCache memBufferCache, InMemoryFreePageManager memFreePageManager,
             ITreeIndexFrameFactory rtreeInteriorFrameFactory, ITreeIndexFrameFactory rtreeLeafFrameFactory,
             ITreeIndexFrameFactory btreeInteriorFrameFactory, ITreeIndexFrameFactory btreeLeafFrameFactory,
-            ILSMIndexFileManager fileManager, TreeIndexFactory<RTree> diskRTreeFactory, IFileMapProvider diskFileMapProvider,
-            ILSMComponentFinalizer componentFinalizer, int fieldCount, IBinaryComparatorFactory[] rtreeCmpFactories,
-            IBinaryComparatorFactory[] btreeCmpFactories, ILinearizeComparatorFactory linearizer,
-            int[] comparatorFields, IBinaryComparatorFactory[] linearizerArray, ILSMFlushController flushController,
-            ILSMMergePolicy mergePolicy, ILSMOperationTracker opTracker, ILSMIOOperationScheduler ioScheduler) {
+            ILSMIndexFileManager fileManager, TreeIndexFactory<RTree> diskRTreeFactory,
+            IFileMapProvider diskFileMapProvider, ILSMComponentFinalizer componentFinalizer, int fieldCount,
+            IBinaryComparatorFactory[] rtreeCmpFactories, IBinaryComparatorFactory[] btreeCmpFactories,
+            ILinearizeComparatorFactory linearizer, int[] comparatorFields, IBinaryComparatorFactory[] linearizerArray,
+            ILSMFlushController flushController, ILSMMergePolicy mergePolicy, ILSMOperationTracker opTracker,
+            ILSMIOOperationScheduler ioScheduler) {
         RTree memRTree = new RTree(memBufferCache, ((InMemoryBufferCache) memBufferCache).getFileMapProvider(),
                 memFreePageManager, rtreeInteriorFrameFactory, rtreeLeafFrameFactory, rtreeCmpFactories, fieldCount,
                 memBtreeFile);
@@ -158,6 +159,7 @@
 
         fileManager.deleteDirs();
         fileManager.createDirs();
+        diskComponents.clear();
     }
 
     @Override