$re = '/^0+?(\d{2})/m';
$str = '001 - Filename 001.mp3
009 - Filename 009.mp3
010 - Filename 010.mp3
060 - Filename 060.mp3
086 - Filename 086.mp3
100 - Filename 100.mp3
1000 - Filename 1000.mp3
01001 - Filename 1001.mp3
01 - Filename with two leading numbers.mp3
1 - Filename with one leading number.mp3';
$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