You want an array of arrays - see perldsc :

use strict;
use warnings; # not use warngings;

my $aoa = [];
## 4 x 4 matrix
for my $x ( 0 .. 3 ){
   for my $y ( 0.. 3){
      $aoa->[$x]->[$y] = "this is a cell!";
   }
}
[download]

HTH!