This produces the desired output for the input you showed:

perl -ple '$_=join",",/\d+/g' input.txt
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But seriously, it seems like you're not telling us the whole story. Not only does this sound like homework, but your example input & output or specification don't indicate:

• whether there can be lines without any of the target characters, and if yes, where they can appear,
• whether there can be any other characters other than the ones you showed on each line, and if yes, where they can appear,
• what happens if the things between the target characters aren't numbers,
• why you said "extract all numbers" but your existing regex appears to only want a specific number of digits.
• There's probably a couple more questions that I'm not thinking of at the moment.
• Update: Are there always three numbers on the line following the single line?

Technically, my example above solves the problem you posed, so if you want a regex that really works for you, you'll have to be a lot more specific.

I'm only getting the first occurrence in {start1}(0-9{2})${end1} (I want to store all matches in the next line)

#!/usr/bin/perl

use strict;
use warnings;

my $content = <<'';
aaa111bbb
ab01ac  d ab02ac ab03ac
aaa222bbb
ab04acab05ac r ab06ac
aaa333bbb
ab01ac t cab06acab10ac

print "$1\n$2,$3,$4\n"
  while $content =~ /aaa(\d+)bbb\nab(\d+)ac.*?ab(\d+)ac.*?ab(\d+)ac/g;
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Thank you!

Hello PetreAdi,

Something like that?

#!/usr/bin/perl

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

my @array = ("aaa111bbb", "ab01ac d ab02ac ab03ac", "aaa222bbb", "ab04
+acab05ac r ab06ac", "aaa333bbb", "ab01ac t cab06acab10ac");

foreach my $str (@array) {
    my @all_nums = $str =~ /(\d+)/g;
    print Dumper \@all_nums;
}

__END__

$ perl test.pl 
$VAR1 = [
          '111'
        ];
$VAR1 = [
          '01',
          '02',
          '03'
        ];
$VAR1 = [
          '222'
        ];
$VAR1 = [
          '04',
          '05',
          '06'
        ];
$VAR1 = [
          '333'
        ];
$VAR1 = [
          '01',
          '06',
          '10'
        ];
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On the Monastery it has been answered before this question (extracting number from string).

I have a variable my $content = get($url) (not array)