$re = '/(.*)\s+S(\d{2})E(\d{2})[\- ]+(.*)/m';
$str = '12 Monkeys S02E10 - Fatherland.txt
Colony S02E01 - Eleven Thirteen.txt
Prison Break S05E05 - Contingency.txt';
$subst = "$1,$2,$3,$4";
$result = preg_replace($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