my $count =0;
    foreach my $column (@{$AoA[$i]}){
            $count ++;
            }
[download]

When all you do in the loop is increment, you might as well just write

    my $count = @{$AoA[$i]};
[download]

which, btw, is approximately N times faster, with N being the size of the array:

use Benchmark 'cmpthese';

my @AoA;
$AoA[42] = [ (1) x 1000 ];

cmpthese(-1,
    {
        counted => sub {
            my $count =0;
            foreach my $column (@{$AoA[42]}){
                    $count ++;
                    }
        },
        direct  => sub {
            my $count = @{$AoA[42]};
        },
    }
);

__END__
             Rate counted  direct
counted   11821/s      --   -100%
direct  9267717/s  78297%      --
[download]