Definitely File::Find will be a good friend to make here. The &wanted sub can deal with collisions on the fly. The following is untested.

use warnings;
use strict;
use File::Find;
use File::Spec::Functions;
use Time::HiRes;
use File::Copy;

my $root = "/path/to/root"
find(\&wanted, $root);
sub wanted {
  if (File::Find::dir eq $root) {
    print "$_ is already in the root folder $root\n";
  } else {
    my $target = catfile($root, $_);
    if (-f $target) {
       my $microtime = join '.', Time::HiRes::gettimeofday();
       print "Filename collision, appending $microtime to $_ before mo
+ving\n";
       move($File::Find::name, $target . $microtime);
    } else {
      print "Moving " . $File::Find::name . " to $target\n";
      move($File::Find::name, $target)
    }
  }
}
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There are probably saner ways to deal with collisions; Being able to know where it came from might be very nice.