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!

After you have created your matrix you probably want to do something with it:) On CPAN there are tons of modules available to work with matrices. As you don't give information what exactly you want to do with your matrix it is impossible to suggest a fitting module. Depending on the content of matrix other implementations might make more sense, e.g. if the matrix is sparse (contains a lot of zeroes).