My first guess is that your printing-loop is incorrect.

for(my $i = 0; $i < @binarray; $i++)
{
    for(my $j = 0; $j < @binarray; $j++)
    {
    print "$binarray[$i][$j]\n";
    }
}
[download]

Is it a fact that the amount of rows is the same as the aoount of columns? (at all times that is).

If it isn't, then you need something like: for (my $j = 0; $j < @{ $binarray[$i] }; ...

Update: Also you are not getting an error, you are getting a warning. And if you want some more information about the erros/warnings you get, you can look in `perldoc perldiag` (the perldiag pod), and/or add 'use diagnostics' to your code. (note the last one should not be used in production code (that is to say, code that is finished))