You state that you want to alter the contents of the files, yet you are not opening them to work on them after you have collected your file listing. Here is one way to alter the contents of each file, but the regex is far to simple in this case, and will probably alter more than it should.

my $base = '/perl/bin/thisdir';
my $count;

opendir(BASE, $base) or die "Cant open $base: $!\n";

for (grep( !/^\./, readdir(BASE) )) {
   open(IN, "$base/$_") or warn "Cant access $_: $!\n" and next;
   while (<IN>) {
      $count += s/old/new/gi;
   }
   close(IN);
}

closedir(BASE);

print "Total changes: $count\n";
[download]

Looking at the code you presented, if you are attempting to actually alter the file names in the directory, you could have the following within the for( readdir ) loop

# snip..
   ( my $newfile = $_ ) =~ s/old/new/;
   rename("$base/$_", "$base/$nwewfile");
# snip..
[download]

Update: Added counting to loop

use perl;