#!/usr/bin/perl -w -i.bak -p
s/<!--#include virtual="(.*)"-->/<?php include(\$_SERVER[\'DOCUMENT_RO
+OT\'].\'$1'); ?>/g;
[download]

Save that and run thescript.pl *.html or find . -iname \*html | xargs thescript.pl That will do the dirty work, but it wont print out the file names for changed files. As for your original script, I don't see where you are printing out the changed lines.