find . -type f -print0|xargs -0 md5sum|sort|perl -ne 'chomp;$ph=$h;($h,$f)=split(/\s+/,$_,2);print "$f"."\x00" if ($h eq $ph)'|xargs -0 rm -v --

That should work. Found it here
http://www.commandlinefu.com/command...directory-tree