You are going line-by-line through each file and replacing the string </script with the string <%--<script . I don't know aspx, but I suspect that's not quite what you want. It seems more likely that your opening comment tag would come before your <script> tag, and a closing one after your </script> tag, but you'll have to show us some sample data to know for sure.

If that's successful, you open a file for appending, but you never write anything to it, and you never write your changed $line anywhere. Presumably you want to write it to a file, and perhaps move that file into the place of the original?

ADDED: One more thing: by using single quotes around your output filename, you prevent interpolation, so you will open a file named $file_name, not test.txt.