Index: trunk/ppStack/src/ppStackCleanup.c
===================================================================
--- trunk/ppStack/src/ppStackCleanup.c	(revision 27329)
+++ trunk/ppStack/src/ppStackCleanup.c	(revision 27343)
@@ -71,4 +71,43 @@
     }
 
+    if (!ppStackFilesIterateUp(config)) {
+        psError(psErrorCodeLast(), false, "Unable to close files.");
+        return false;
+    }
+    ppStackFileActivation(config, PPSTACK_FILES_STACK, false);
+    ppStackFileActivation(config, PPSTACK_FILES_PHOT, false);
+
+    // Ensure files are freed
+    {
+        options->outRO->data_exists = false;
+        options->outRO->parent->data_exists = false;
+        options->outRO->parent->parent->data_exists = false;
+        psFree(options->outRO);
+        options->outRO = NULL;
+
+        pmFPAview *view = pmFPAviewAlloc(0);// Pointer into FPA hierarchy
+        view->chip = view->cell = 0;        // pmFPAviewFreeData doesn't want to deal with readouts
+        pmFPAfile *jpeg1 = pmFPAfileSelectSingle(config->files, "PPSTACK.OUTPUT.JPEG1", 0); // JPEG file
+        pmFPAviewFreeData(view, jpeg1);
+        pmFPAfile *jpeg2 = pmFPAfileSelectSingle(config->files, "PPSTACK.OUTPUT.JPEG2", 0); // JPEG file
+        pmFPAviewFreeData(view, jpeg2);
+        pmFPAfile *phot = NULL;         // Photometry file
+        if (options->photometry) {
+            phot = pmFPAfileSelectSingle(config->files, "PSPHOT.INPUT", 0); // Photometry file
+            pmFPAviewFreeData(view, phot);
+        }
+
+        view->readout = 0;
+        pmReadout *ro1 = pmFPAviewThisReadout(view, jpeg1->fpa); // JPEG readout
+        ro1->data_exists = ro1->parent->data_exists = ro1->parent->parent->data_exists = false;
+        pmReadout *ro2 = pmFPAviewThisReadout(view, jpeg2->fpa); // JPEG readout
+        ro2->data_exists = ro2->parent->data_exists = ro2->parent->parent->data_exists = false;
+        if (options->photometry) {
+            pmReadout *ro = pmFPAviewThisReadout(view, phot->fpa); // Photometry readout
+            ro->data_exists = ro->parent->data_exists = ro->parent->parent->data_exists = false;
+        }
+        psFree(view);
+    }
+
     return true;
 }