It depends on the files that it said were uncleanable. If some are Windows OS files then you need to extract new copies from your Windows CD. If they are user files, then delete them.
Did it find any virus and clean it up prior to mentioning the uncleanable files? If not, did it mention what virus you had in the past that infected the files or did it say your currently infected with a virus that it can't clean using the online scan?
If you want us take a look and see if you appear to be infected, do this
Go <a href=http://home.earthlink.net/~rmbox/Reticulated/Only_IE.html> here </a>and download Startlog.com
Once it's downloaded, double left click on it to execute it. You'll see a Notepad window open up. Close the window. Now on your Desktop you should see a light blue icon called Startup.log
Right click on it and select Rename. Now rename it Startup.txt
When prompted if your sure you want to do this, click on Yes.
Now come back here and click on PostReply. At the bottom of the reply window click on "Browse". Now locate Startup.txt in the Explorer window and double left click on it to attach the Startup.txt file.