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 454db50..2ae7ca0 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
@@ -109,6 +109,7 @@
     @Override
     public void create(int indexFileId) throws HyracksDataException {
         memBTree.create(indexFileId);
+        fileManager.removeDirs();
         fileManager.createDirs();
     }
 
diff --git a/hyracks-storage-am-lsm-common/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/common/api/ILSMFileManager.java b/hyracks-storage-am-lsm-common/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/common/api/ILSMFileManager.java
index 7ba0198..eb71704 100644
--- a/hyracks-storage-am-lsm-common/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/common/api/ILSMFileManager.java
+++ b/hyracks-storage-am-lsm-common/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/common/api/ILSMFileManager.java
@@ -32,6 +32,8 @@
  */
 public interface ILSMFileManager {
     public void createDirs();
+    
+    public void removeDirs();
 
     public FileReference createFlushFile(String relFlushFileName);
 
diff --git a/hyracks-storage-am-lsm-common/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/common/impls/LSMTreeFileManager.java b/hyracks-storage-am-lsm-common/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/common/impls/LSMTreeFileManager.java
index 0334a8e..fdd3b74 100644
--- a/hyracks-storage-am-lsm-common/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/common/impls/LSMTreeFileManager.java
+++ b/hyracks-storage-am-lsm-common/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/common/impls/LSMTreeFileManager.java
@@ -64,7 +64,6 @@
         this.fileMapProvider = fileMapProvider;
         this.ioManager = ioManager;
         this.baseDir = baseDir;
-        createDirs();
     }
 
     @Override
@@ -75,6 +74,22 @@
         }
     }
 
+    @Override
+    public void removeDirs() {
+        for (IODeviceHandle dev : ioManager.getIODevices()) {
+            File f = new File(dev.getPath(), baseDir);
+            if (f.exists() && f.isDirectory()) {
+                // Delete the files in the directory first
+                for (File fileInDir : f.listFiles()) {
+                    fileInDir.delete();
+                }
+            }
+
+            // Delete the directory
+            f.delete();
+        }
+    }
+
     public FileReference createFlushFile(String relFlushFileName) {
         // Assigns new files to I/O devices in round-robin fashion.
         IODeviceHandle dev = ioManager.getIODevices().get(ioDeviceIndex);