$re = '/(?:\[#\d+\K,|(?<!^)\G,)(#\d+)/';
$str = '#2335, IFCRELASSOCIATESMATERIAL, \'2ON6$yXXD1GAAH8whbdZmc\', #5,$,$, [#40,#221,#268,#281],#2334';
$subst = "_$1";
$result = preg_replace($re, $subst, $str);
echo "The result of the substitution is ".$result;
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