the rogue anti-virus probably placed all your files as hidden
to revert this, do the following
Windows xp:

Windows Vista/7:
Click on start - Control panel - Appearance and Personalization - Folder Options - Then do the same as in the picture
you'll be able to see all you're hidden file, then all you have to do is go in c:\ and rightclick program files and select properties
then uncheck where it says Hidden, it will say do you want to do this do all files/folder, say yes. i'm not 100% sure, but i think you'll had to do this for all your other files/folder
Since you've only been on trusted sites, you probably have a dialer / backdoor / DNS hijacker of some sort on you're comp. They simply wont stop downloading malware/viruses on your comp until you get rid of it.
like other said, run malwarebytes, spybot, ad-aware
superantispyware might also be useful.
do a full scan with your anti-virus.
download tdsskiller, if tdsskiller finds nothing, try Sophos Anti-Rootkit
check your DNS settings
start - control panel - network connections - local area connection - general tab (properties) - click once on Internet Protocol (TCP/IP) then Properties - Obtain DNS server address automatically
if you need more help, simply pm me
good luck