diff --git a/invesalius/data/floodfill.pyx b/invesalius/data/floodfill.pyx
index 5b7ac6e..6636cc9 100644
--- a/invesalius/data/floodfill.pyx
+++ b/invesalius/data/floodfill.pyx
@@ -6,6 +6,7 @@ from collections import deque
 
 from cython.parallel import prange
 from libc.math cimport floor, ceil
+from libcpp cimport bool
 from libcpp.deque cimport deque as cdeque
 from libcpp.vector cimport vector
 
@@ -237,22 +238,37 @@ def floodfill_auto_threshold(np.ndarray[image_t, ndim=3] data, list seeds, float
 @cython.wraparound(False)
 @cython.nonecheck(False)
 def fill_holes_automatically(np.ndarray[mask_t, ndim=3] mask, np.ndarray[np.uint16_t, ndim=3] labels, unsigned int nlabels, unsigned int max_size):
-        cdef np.ndarray[np.uint32_t, ndim=1] sizes = np.zeros(shape=(nlabels + 1), dtype=np.uint32)
-        cdef int x, y, z
-        cdef int dx, dy, dz
+    """
+    Fill mask holes automatically. The hole must <= max_size. Return True if any hole were filled.
+    """
+    cdef np.ndarray[np.uint32_t, ndim=1] sizes = np.zeros(shape=(nlabels + 1), dtype=np.uint32)
+    cdef int x, y, z
+    cdef int dx, dy, dz
+    cdef int i
+
+    cdef bool modified = False
+
+    dz = mask.shape[0]
+    dy = mask.shape[1]
+    dx = mask.shape[2]
+
+    for z in xrange(dz):
+        for y in xrange(dy):
+            for x in xrange(dx):
+                sizes[labels[z, y, x]] += 1
 
-        dz = mask.shape[0]
-        dy = mask.shape[1]
-        dx = mask.shape[2]
+    #Checking if any hole will be filled
+    for i in xrange(nlabels + 1):
+        if sizes[i] <= max_size:
+            modified = True
 
-        for z in xrange(dz):
-            for y in xrange(dy):
-                for x in xrange(dx):
-                    sizes[labels[z, y, x]] += 1
+    if not modified:
+        return 0
 
+    for z in prange(dz, nogil=True):
+        for y in xrange(dy):
+            for x in xrange(dx):
+                if sizes[labels[z, y, x]] <= max_size:
+                    mask[z, y, x] = 254
 
-        for z in prange(dz, nogil=True):
-            for y in xrange(dy):
-                for x in xrange(dx):
-                    if sizes[labels[z, y, x]] <= max_size:
-                        mask[z, y, x] = 254
+    return modified
diff --git a/invesalius/data/mask.py b/invesalius/data/mask.py
index 07c172d..d00d22e 100644
--- a/invesalius/data/mask.py
+++ b/invesalius/data/mask.py
@@ -353,9 +353,13 @@ class Mask():
 
             imask = (~(matrix > 127))
             labels, nlabels = ndimage.label(imask, bstruct, output=np.uint16)
-            print ">>>>", nlabels
-            floodfill.fill_holes_automatically(matrix, labels, nlabels, size)
-            self.save_history(index, orientation, self.matrix.copy(), cp_mask)
+
+            if nlabels == 0:
+                return
+
+            ret = floodfill.fill_holes_automatically(matrix, labels, nlabels, size)
+            if ret:
+                self.save_history(index, orientation, self.matrix.copy(), cp_mask)
         else:
             bstruct = ndimage.generate_binary_structure(2, CON2D[conn])
 
@@ -371,11 +375,15 @@ class Mask():
             imask = (~(matrix > 127))
             labels, nlabels = ndimage.label(imask, bstruct, output=np.uint16)
 
+            if nlabels == 0:
+                return
+
             labels = labels.reshape(1, labels.shape[0], labels.shape[1])
             matrix = matrix.reshape(1, matrix.shape[0], matrix.shape[1])
 
-            floodfill.fill_holes_automatically(matrix, labels, nlabels, size)
-            self.save_history(index, orientation, matrix.copy(), cp_mask)
+            ret = floodfill.fill_holes_automatically(matrix, labels, nlabels, size)
+            if ret:
+                self.save_history(index, orientation, matrix.copy(), cp_mask)
 
     def __del__(self):
         if self.is_shown:
diff --git a/invesalius/gui/frame.py b/invesalius/gui/frame.py
index 1c97e67..b6c4bab 100644
--- a/invesalius/gui/frame.py
+++ b/invesalius/gui/frame.py
@@ -596,7 +596,6 @@ class Frame(wx.Frame):
         Publisher.sendMessage('Enable style', const.SLICE_STATE_MASK_FFILL)
 
     def OnFillHolesAutomatically(self):
-        #  Publisher.sendMessage('Fill holes automatically')
         fdlg = dlg.FillHolesAutoDialog(_(u"Fill holes automatically"))
         fdlg.Show()
 
@@ -752,20 +751,23 @@ class MenuBar(wx.MenuBar):
         self.clean_mask_menu.Enable(False)
 
         mask_menu.AppendSeparator()
+
         self.fill_hole_mask_menu = mask_menu.Append(const.ID_FLOODFILL_MASK, _(u"Fill holes manually"))
         self.fill_hole_mask_menu.Enable(False)
 
         self.fill_hole_auto_menu = mask_menu.Append(const.ID_FILL_HOLE_AUTO, _(u"Fill holes automatically"))
         self.fill_hole_mask_menu.Enable(False)
 
+        mask_menu.AppendSeparator()
+
         self.remove_mask_part_menu = mask_menu.Append(const.ID_REMOVE_MASK_PART, _(u"Remove parts"))
         self.remove_mask_part_menu.Enable(False)
 
         self.select_mask_part_menu = mask_menu.Append(const.ID_SELECT_MASK_PART, _(u"Select parts"))
         self.select_mask_part_menu.Enable(False)
-    
+
         mask_menu.AppendSeparator()
-        
+
         self.crop_mask_menu = mask_menu.Append(const.ID_CROP_MASK, _("Crop"))
         self.crop_mask_menu.Enable(False)
 
--
libgit2 0.21.2