There's a number of improvements you could make. Here's a (not necessarily complete) list:

• Deferencing variables has an overhead. Use a hash instead of a reference to a hash.
• You're getting a list of keys three times and sorting those lists twice. Just do all of this once.
• There's a builtin module List::Util which provides a max() function. There's no need roll your own code for this. [As far as I know, all of the functions provided by that module are implemented in C, so you also get a performance bonus.] (See also: List::MoreUtils)
• Transforming the hash into an AoA is unnecessary. All the required functionality can be achieved by just using the initial hash.
• You've used a total of four foreach loops; in the code I've shown below there's only one. [for and foreach are synonymous: save yourself some typing by just using for]
• You can use the -l (ell) command switch so you don't need $/ (or "\n") after each print (see perlrun: Command Switches).

I took your original spec and produced the following script. While I kept to the spec, I made no any attempt to reproduce any parts of your script.

#!/usr/bin/env perl -l

use strict;
use warnings;

use List::Util qw{max};

my %Hash = (
    "A" => ["HYU"],
    "B" => ["TU6"],
    "C" => [ "11", "09", "88", "2" ],
    "D" => [ "01", "11" ]
);

my @keys = sort keys %Hash;

print join ",\t" => @keys;

{
    no warnings 'uninitialized';

    for my $i (0 .. max map { $#{$Hash{$_}} } @keys) {
        print join "\t" => map { $Hash{$_}[$i] } @keys;
    }
}
[download]

Output:

A,      B,      C,      D
HYU     TU6     11      01
                09      11
                88      
                2
[download]

Using tabs for the output worked in this instance; however, with other data, columns may be out of alignment. Also, tab widths can vary; so what looks fine here may be misaligned elsewhere. Consider using printf to format your output.

Also have a read of "Perl Performance and Optimization Techniques" for more tips you can use in your other scripts.

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