When USB drives are plugged into multiple computers, there is a high chance of being infected with viruses. Public computer shop like printing and internet cafes are often places you can be sure to get your pen drives infected.
While each virus is different, it is very common to see them infect autorun.inf files in the usb drive and then use that loophole to infect other files. Recently, I faced one such virus that spread from a USB drive to my entire network and all I could see was shortcuts to the files. The shortcuts were actually to a program, all the files were missing, I even tried looking for hidden files but there werent any ! The free space available on these hard disks showed that the data was still present somewhere. I took a look at the drive through command prompt (Run > cmd > dir -ah). There I could see that the folders were present on the drives, they had been marked as system protected and Windows 7 wasnt showing these folders.
How to fix Cannot see files on usb drive
Open the drive in My computer ( Windows Explorer )
Press Alt > Tools > Folder Options > View > Uncheck Hide protected operating system files
Also click Show Hidden files. You should be able to see the hidden folders and files.
If you have a lot of shortcuts in the drive, go to search and type *.lnk, now delete these useless shortcuts.
Now its time to fix the folders and files on this drive.
Click Start and type in CMD, press enter (run as administrator if required)
Go to the infected drive by typing D: (replace D with the drive that is infected)
Type dir -ah to see all the hidden folders
type attrib -r -a -s -h d:\(folder name). This needs to be typed for each hidden folder
You can also try attrib -h -r -s /s /d D:\*.*
Preventing future infections
Install Panda USB Vaccine. It protects your USB drive from infections by making your autorun.inf immune to infections.
Install a good antivirus. Microsoft Security Essentials is recommended if you have genuine Windows. Else install a good free antivirus like Avast, Aviara or Commodo.