diff --git a/common/source/java/ch/systemsx/cisd/common/Constants.java b/common/source/java/ch/systemsx/cisd/common/Constants.java
index ddfb5d628e1f4cd7322dae32556fd5f4286a9c77..1306a277a0d595e19b9d7aa379623c4bf667b8d0 100644
--- a/common/source/java/ch/systemsx/cisd/common/Constants.java
+++ b/common/source/java/ch/systemsx/cisd/common/Constants.java
@@ -24,7 +24,13 @@ package ch.systemsx.cisd.common;
 public class Constants
 {
 
+    /** String that indicates a marker file */
+    public static final String MARKER_PREFIX = ".MARKER_";
+    
     /** The prefix of marker files that indicate that the processing of some path is finished. */
-    public static final String IS_FINISHED_PREFIX = ".is_finished_";
+    public static final String IS_FINISHED_PREFIX = MARKER_PREFIX + "is_finished_";
+
+    /** The prefix of marker files that indicate that the processing of some path is finished. */
+    public static final String DELETION_IN_PROGRESS_PREFIX = MARKER_PREFIX + "deletion_in_progress_";
 
 }
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTask.java b/common/source/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTask.java
index 6972b5db29efae792c9f302e0206f1eb66b06f7a..c3b890023cd91a3b1969f950561b237ea39b86df 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTask.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTask.java
@@ -26,6 +26,7 @@ import java.util.TimerTask;
 import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
 
+import ch.systemsx.cisd.common.Constants;
 import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
 import ch.systemsx.cisd.common.logging.ISimpleLogger;
 import ch.systemsx.cisd.common.logging.LogCategory;
@@ -202,7 +203,10 @@ public final class DirectoryScanningTimerTask extends TimerTask implements ISelf
         { // Guard: skip faulty paths.
             return;
         }
-
+        if (isMarker(path))
+        {
+            return;
+        }
         try
         {
             final boolean handledOK = handler.handle(path);
@@ -220,6 +224,11 @@ public final class DirectoryScanningTimerTask extends TimerTask implements ISelf
         }
     }
 
+    private static boolean isMarker(File path)
+    {
+        return path.getName().startsWith(Constants.MARKER_PREFIX);
+    }
+    
     private void addToFaultyPaths(File path)
     {
         faultyPaths.add(path);