Looking more closely at this version of your code, I'm wondering...

• Why do you do mkdir( "directory$dir",0755 ); and then turn right around and chmod that new directory to 0777? Why not just tell mkdir to use the intended permissions in the first place? (As it turns out, 0777 is said to be the default setting for mkdir.)
• Even if you really had to do chmod on files or directories, why use a system call for that? Is there some problem with using the perl built-in chmod function? (I would expect it to work in an OS-independent manner.)
• Why do the if ($^O =~ /Win32/) branching so many times? I think the two points above would eliminate most of the OS-dependent branching, but if you really still have some points where you need to branch, group those things together a little more, to minimize the number of conditional blocks, and make the code easier to read/maintain.
• It looks like you may be lacking some OS-dependent branching that should be there (near the beginning, where your "die" messages always have backslash paths, regardless of OS).

If you were to use File::Spec (as suggested above), here's how the code would start out:

use strict;
use warnings;
use Cwd;
use Getopt::Long;
use File::Spec;   # this will automatically load OS-appropriate functi
+ons

# ... [snip] ...

# Get the current working directory
my $home_dir = getcwd;

# Change to the test directory
chdir($testdir) or die "$0: chdir $testdir: $!";

# Set up test dirs if they do not exist
for my $t ( qw/test test1/ ) {
    mkdir $t or die "mkdir ". File::Spec->catfile($testdir, $t) .": $!
+\n";
}

# Change to the test area
chdir("test") or die "chdir test: $!\n";

# Directory Manipulation
for my $dir ( 0 ..  $num-1 ) {
    my $dirname = "directory$dir";

    # Make the directory
    if (!-d $dirname ) {
        mkdir $dirname or 
            die "mkdir ". File::Spec->catfile( $testdir, "test", $dirn
+ame ) .": $!\n";
    }
    #...
[download]

I hope that gets the general idea across. It looks like your script is simply meant to check that certain operations work as hoped for, and doesn't really accomplish anything other than testing, so I won't pursue it further.

I'll just emphasize that you should use perl built-in functions and core modules (e.g. File::Copy whenever they are available, rather than system calls to shell commands -- perl already provides a lot of OS-independence for you, and you'll have fewer problems and less code to write that way.

If you really must use system calls to run OS-dependent tools, modularize and/or group those things so that they hang together for each OS. Your code tests the OS type in five different places, and you shouldn't have to do that test more than once (or not at all, with proper use of existing modules).