New symptom...new malware?

one week ago, my friend called me to help him with his usb hd... he told me that his pc was infected with virus
he scanned all his computer and external stuff, and freed them from virii
his folders on that hd was disappeared though size still same
first i thought it was just an usual problem...disabled showing hidden files
but this time was different ...it was checked to show all files even protected system file ...yet nothing shown
i brought that usb hd... and examined it ..what to surprise it was like clean ...but size still same...tried some hex editor for disks...the files still there ..nothing encrypted or corrupted even
when i tried to create or copy new file to hd in the main root, i got an error about corruption of the disk
though there was only one folder, when i try to copy or do whatever inside it ..i can do it simply ..but not in the main root
today my other friend...got the same symptom ..his computer was infected and folder and files on his fixed hard disappeared

anyone heard about this before? how can i fix this thing?
thanks in advance

 

Can you right click on the drive - properties - Tools tab and select "Check now" for errors which should run a chkdsk on it?

 

thanks for respond ...actually i did that and got some errors..i tried the command with /F parameter trying to fix errors ..but it didnt work ..it tells me that operation cant be done because its used and i need to dismount it first
maybe i try that command on livecd
but is there any other suggestion for now?