Use references right from the start. There's no need for an intermediate array. I think you would benefit from reading the following (in this order): perlreftut, perllol, and perldsc. References are also discussed in great depth in perlref, but the first three docs I mentioned are easier reads, and will get you going in the right direction.

use strict;
use warnings;
use Data::Dumper;

my @parsed_table = map { [ split /,/ ] } FilterData( 2, 0 );

print Dumper \@parsed_table;
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