string ss = "<script alsdf>***lsdkjf </script>aaa<script >";

            Regex reg = new Regex("<.*?script.*?>", RegexOptions.IgnoreCase);

            Match m = reg.Match(ss);

            while (m.Success) {
                ss = reg.Replace(ss, "[script]");
                m = m.NextMatch();

            }
            Console.Write(ss);

------解决方案--------------------
new Regex(@"<script.*?>(.*?)</script>",  RegexOptions.Multiline | RegexOptions.IgnoreCase);  

这样可以