To test whether some "file" is a directory, this logic will work:

   
 if (-d $filename) { 
   print "directory\n"; 
 } else { 
   print "other\n";
 }
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So if you have @filenames, you can filter it into @files and @dirs with this sub:

  sub filter_names {
    my ($nref,$fref,$dref) = @_;
    for (@$nref) {
      if (-d) {
        push @$dref, $_;
      } else {
        push @$fref, $_;
      }
    }
  }
[download]

Call it like:
filter_names(\@filenames,\@files,\@dirs);

that ok?
Update: Oops Chmrr said the same thing already... sorry.