Hidden and system files have appeared all over my system?

Hi there! I use a Window VISTA based PC. I cant recollect that what happened but files like desktop.ini and recycler$ , config.msi and lots of .sys files now seem to be in my hard disk partitions and personal folder. More annoying are the numerous undesired and unwanted shortcuts that have also appeared in the system. I am just this sure that I didnt touched the registry or anything sensitive.What to do to make it as it was before. lol, thanks in advance.