php > preg_match_all("/^\s*(#+)\s*(.*)$/m", $txt, $matches);
php > print_r($matches);
Array
(
    [0] => Array
        (
            [0] => # Main Title
            [1] =>
## Level 1.1
            [2] =>
### Level 2.1
            [3] =>
#### Level 3.1
            [4] =>
#### Level 3.2
            [5] =>
#### Level 3.3
            [6] =>
### Level 2.2.
            [7] =>
### Level 2.3.
            [8] =>
## Level 1.2
            [9] =>
## Level 1.3
        )

    [1] => Array
        (
            [0] => #
            [1] => ##
            [2] => ###
            [3] => ####
            [4] => ####
            [5] => ####
            [6] => ###
            [7] => ###
            [8] => ##
            [9] => ##
        )

    [2] => Array
        (
            [0] => Main Title
            [1] => Level 1.1
            [2] => Level 2.1
            [3] => Level 3.1
            [4] => Level 3.2
            [5] => Level 3.3
            [6] => Level 2.2.
            [7] => Level 2.3.
            [8] => Level 1.2
            [9] => Level 1.3
        )

)