$re = '/\[([^][]+)]\((?![^()]*\bnotes\.md\b)[^()]*\)/m';
$str = '[Item 1](./path/notes.md)
[Item 2](./path)
[Item 3](./path/notes.md)
[Item 4](./path)';
preg_match_all($re, $str, $matches, PREG_SET_ORDER, 0);
// Print the entire match result
var_dump($matches);
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php