there's a very popular virus that does this, its a rogue anti-virus (fake anti-virus) that places all your files as hidden to scare the user
make sure you do not have this (it should display a lot of fake alerts)
to view your hidden files, do this
rightclick start - explore

if your using vista/7, go in control panel, folder options (classic view) and do above
to unhide your files, simply rightclick them and uncheck Hidden
do this to the folders
lmk if it works