use Data::Dumper;

my @array;
# read from the file handle line by line
while(<DATA>) {
  chomp;

  # split each line by ',' and save
  # corresponding records into the @recs array
  my @recs = split /\,/;

  # loop through the records array..
  for (my $i; $i < @recs; $i++) {

    # and save I-th record in array
    # array[I].  Use @{..} to let push() know
    # that array[I] is also an array.
    push @{$array[$i]}, $recs[$i];
  }
}

print Dumper(\@array);

__DATA__
A,B,C
D,B,C

E,C,C

##</code><code>##

$VAR1 = [
          [
            'A',
            'D',
            'E'
          ],
          [
            'B',
            'B',
            'C'
          ],
          [
            'C',
            'C',
            'C'
          ]
        ];