diff --git a/sys/filesys_windows.go b/sys/filesys_windows.go
index fdfab4620..1c3cc40ac 100644
--- a/sys/filesys_windows.go
+++ b/sys/filesys_windows.go
@@ -278,12 +278,22 @@ func ForceRemoveAll(path string) error {
 func cleanupWCOWLayers(root string) error {
 	// See snapshots/windows/windows.go getSnapshotDir()
 	var layerNums []int
+	var rmLayerNums []int
 	if err := filepath.Walk(root, func(path string, info os.FileInfo, err error) error {
 		if path != root && info.IsDir() {
-			if layerNum, err := strconv.Atoi(filepath.Base(path)); err == nil {
-				layerNums = append(layerNums, layerNum)
+			name := filepath.Base(path)
+			if strings.HasPrefix(name, "rm-") {
+				layerNum, err := strconv.Atoi(strings.TrimPrefix(name, "rm-"))
+				if err != nil {
+					return err
+				}
+				rmLayerNums = append(rmLayerNums, layerNum)
 			} else {
-				return err
+				layerNum, err := strconv.Atoi(name)
+				if err != nil {
+					return err
+				}
+				layerNums = append(layerNums, layerNum)
 			}
 			return filepath.SkipDir
 		}
@@ -293,8 +303,14 @@ func cleanupWCOWLayers(root string) error {
 		return err
 	}
 
-	sort.Sort(sort.Reverse(sort.IntSlice(layerNums)))
+	sort.Sort(sort.Reverse(sort.IntSlice(rmLayerNums)))
+	for _, rmLayerNum := range rmLayerNums {
+		if err := cleanupWCOWLayer(filepath.Join(root, "rm-"+strconv.Itoa(rmLayerNum))); err != nil {
+			return err
+		}
+	}
 
+	sort.Sort(sort.Reverse(sort.IntSlice(layerNums)))
 	for _, layerNum := range layerNums {
 		if err := cleanupWCOWLayer(filepath.Join(root, strconv.Itoa(layerNum))); err != nil {
 			return err