I have had real good luck by removing the supers during the evening
hours and collecting them early the following morning before the hives
become too active.  The supers without brood are usually bee free and
what few frames that have bees covering brood (usually drone brood) are
quickly taken care of with either smoke, the bee brush or are left out
to be clean up by robbers.  No mess, no stink and best of all, no mad
bees.