there are so many things wrong with this that i am not sure where to begin. no AV, no firewall??? what system are you running and how is it running?windows OS? on a 56k or some sort of broadband connection(God forbid) is your machine one of the zombies that tries to crack mine at least 3or 4 times a day? there is a reason why the rest of us run firewalls, proxies spend huge amounts of time (and money, sometimes...ESPECIALLY IN CLEANING UP THE AFTERMATH OF A SECURITY BREACH). there is a saying out there, "if you are not part of the solution then you are part of the problem". as we speak my firewall deflects yet another helkern attack. if i go to my firewall records i can find thirty or forty instances from the past few days, of this same attack, by about 7 or 8 different IP's.several different machines who's owners are probobly blissfully unaware that their machines are being remotely used to try to subvert others out there, along with mine. they might have been just like yourself, criminally irresponsible in leaving the armory (your PC) sitting there wide open and unlocked( no firewall,IDS,AV)so that joe cyber-terrorist( aka joe script kiddie) can run his programs on your machine every time it connects to the internet and use your processing power, bandwidth and information etc etc to snipe at the rest of us.
please, for your own sake and that of any one else out here, protect us all and lock up yer damn gun!
as for the fella whose question you were trying to answer, if the file system canbe accessed by the infected computer ( a live connection of any sort) than it can be affected, if the virus/worm/trojan is targeted at that file type.i guess i would have to say that some sort of inert media is your best bet for secure data storage(floppy/cd/etc).