I have no idea what 'there' you are talking about, but here is code that will build the arrays.

#!/usr/bin/perl -w

use PDL;
$matrixfile = $ARGV[0];
open(MATRIX, "$matrixfile") || die "Error: Can't open $matrixfile file
+ for reading: $!\n";

@matrix = map({chomp; [split(/\s+/, $_)]} <MATRIX>);

for my $ctl (
 [ qw ( 0 1 2 3 ) ],
 [ qw ( 4 1 2 3 ) ],
 [ qw ( 0 4 2 3 ) ],
 [ qw ( 0 1 4 3 ) ],
 [ qw ( 0 1 2 4 ) ],
) {
    for my $data (@matrix) {
        for my $offset (@$ctl) {
            print $data->[$offset], ' ';
        }
        print "\n";
    }
    print "\n";
}
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If you replace the print functions with pushes into an array you should end up with what you want.