#!/usr/bin/perl
my $dir = '/your/directory';

package MyFile;
use Digest::MD5;

sub new {
  my ( $class, $name ) = @_;
  my $self = { name => $name };
  bless $self, $class;
}

sub name { $_[0]->{name} }

sub md5 {
  my $self = shift;
  $self->{md5} ||= do {
    open my $fh, "<", $self->name or die $!;
    binmode $fh;
    Digest::MD5->new->addfile($fh)->digest;
  };
}

package main;
use File::Find;
my %files;

File::Find::find(
  {
    wanted => sub {
      -f && push @{ $files{ -s _ } }, MyFile->new($File::Find::name);
      }
  },
  $dir
);

my @drop;
for ( keys %files ) {
  my %t;
  if ( @{ $files{$_} } > 1 ) {
    for ( @{ $files{$_} } ) {
      push @drop, $_->name if $t{ $_->md5 }++;
    }
  }
}

local $, = $/;
print @drop;