diff --git a/isicle/md.py b/isicle/md.py
index 6f7d3f4..8696ecc 100644
--- a/isicle/md.py
+++ b/isicle/md.py
@@ -375,6 +375,9 @@ def finish(self):
         # Get list of outputs
         outfiles = glob.glob(os.path.join(self.temp_dir, "*"))
 
+        # Filter directories
+        outfiles = [x for x in outfiles if not os.path.isdir(x)]
+
         # Result container
         result = {}