<?php

$str = "Lorem ipsum [1. dolor sit amet, [consectetuer adipiscing] elit.]. Aenean commodo ligula eget dolor.[2. Dolor, [consectetuer adipiscing] elit.] Aenean massa[3. Lorem ipsum] dolor.";
preg_match_all('/\[(?>[^\[\]]|(?R))*]/', $str, $matches);
$res = array_map(function($el) {
	return preg_replace('/^\[\d+\.(.*?)\s*\]$/s', '$1', $el); 
	},
	$matches[0]);
print_r($res);