You were actually right and the data structure is a hash of two dimentional arrays, although a more Perlish expression might be array of array refs. By the way, the index of the second dimention is getting from a hash of hash refs.

You can easily visualize this with the help of Data::Dumper:

use Data::Dumper;

use strict;
use warnings;

my $file = "afile";
my $alias = "somealias";
my %num;
my %val;
$num{$alias}{save} = 2;
$val{$file}[3][$num{$alias}{save}] = 1;
print Dumper(\%val);
[download]

$VAR1 = {
          'afile' => [
                       undef,
                       undef,
                       undef,
                       [
                         undef,
                         undef,
                         1
                       ]
                     ]
        };
[download]