You need to run this script after you log in with ssh and have the command prompt.
This will not prevent future attacks, it just helps in removing all segments of the code from your files. Look at the thrid post from Jan talking about securing your site from future attacks. If your files are already cleared out than you need to take a look at those links and make sure you dont have security issues with your plugins or .htaccess files. Also check your mySQL users and make sure you recognize all of them. This can be another culprit for malware.
@tekno23
Man you rock. My work has a VPS with over 50 wordpress installs and most of them were infected that perl script saved my life and at least a days worth of work. AWESOME!