Always seeing hidden files? How to fix it?

Hello,

Okay, so what happened was a fellow classmate asked me to copy a lecture onto her memory stick. When I did found a W32.SillyFDC. It was detected and removed shortly after. Afterwards though, something weird happened. I had to restart my computer in order for the removal to take effect. After I restarted it I found two "hidden" files on my desktop. They were hidden, they were supposed to be hidden, but they were clearly visible. I browsed through my Windows folder and loaded a few word documents and the temp files were visible, a whole bunch of files and folders that were NOT supposed to be able to be seen, were visible and still "hidden"! Is there any way to fix this without reformatting my laptop? It's starting to get really annoying seeing all of these "hidden" files. I also ran a full system scan of my whole computer and it hasn't found any problems at all.