diff --git a/hyracks-storage-am-lsm-btree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/btree/dataflow/LSMBTreeDataflowHelper.java b/hyracks-storage-am-lsm-btree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/btree/dataflow/LSMBTreeDataflowHelper.java
index 5bb5308..fe4cdc2 100644
--- a/hyracks-storage-am-lsm-btree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/btree/dataflow/LSMBTreeDataflowHelper.java
+++ b/hyracks-storage-am-lsm-btree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/btree/dataflow/LSMBTreeDataflowHelper.java
@@ -58,6 +58,9 @@
                 memNumPages);
         IFileSplitProvider fileSplitProvider = opDesc.getFileSplitProvider();
         FileReference file = fileSplitProvider.getFileSplits()[partition].getLocalFile();
+        if (file.getFile().exists() && !file.getFile().isDirectory()) {
+            file.delete();
+        }
         InMemoryFreePageManager memFreePageManager = new InMemoryFreePageManager(memNumPages, metaDataFrameFactory);
         return LSMBTreeUtils.createLSMTree(memBufferCache, memFreePageManager, (IOManager) ctx.getIOManager(), file
                 .getFile().getPath(), opDesc.getStorageManager().getBufferCache(ctx), opDesc
diff --git a/hyracks-storage-am-lsm-rtree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/rtree/dataflow/LSMRTreeDataflowHelper.java b/hyracks-storage-am-lsm-rtree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/rtree/dataflow/LSMRTreeDataflowHelper.java
index 8bd6f02..4f9280d 100644
--- a/hyracks-storage-am-lsm-rtree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/rtree/dataflow/LSMRTreeDataflowHelper.java
+++ b/hyracks-storage-am-lsm-rtree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/rtree/dataflow/LSMRTreeDataflowHelper.java
@@ -71,6 +71,9 @@
                 memNumPages);
         IFileSplitProvider fileSplitProvider = opDesc.getFileSplitProvider();
         FileReference file = fileSplitProvider.getFileSplits()[partition].getLocalFile();
+        if (file.getFile().exists() && !file.getFile().isDirectory()) {
+            file.delete();
+        }
         InMemoryFreePageManager memFreePageManager = new LSMRTreeInMemoryFreePageManager(memNumPages,
                 metaDataFrameFactory);
         return LSMRTreeUtils.createLSMTree(memBufferCache, memFreePageManager, (IOManager) ctx.getIOManager(), file