I noticed the "?" mark too. Check the "all_control.txt" file to see if it has any extra formatting characters. Then the following should work fine.

#!/usr/bin/perl

use strict;

my $file = "all_controls.txt";

open(FILE, "<$file") || die "Unable to open $file: $!\n";
my @file_contents = <FILE>;
foreach (@file_contents) {
   chomp;
   $_ =~ /^(.*?)\..*?$/; # remove filename extension after '.'
   mkdir ($1, 0755) || die "Unable to create directory: $!\n";
   print "Created directory: $1\n" if (! $@);
}

# end
[download]

Edit: g0n - code tags