#! /usr/bin/perl
use strict;
use warnings;


my $AoA = [];
my $i;
while ( my $line = <DATA> ) {
        chomp $line;
        if ( $line eq '#' ) {
                $i += defined $i ? 1 : 0;
        }
        else {
                $i = 0  if !defined $i;
                push @{$AoA->[$i]}, $line;
        }
}

require Data::Dumper;
print Data::Dumper->new( [ $AoA ], [ '*AoA' ] )->Dump();

        

__DATA__
#
Zeile 1
Zeile 2
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#
Zeile 5