Ahh, the shortcut virus, really easy to remove.
The folder option might not work, as the virus could have been infected the machine, thus disabling you to see infected files.
And as it was in my case, that hidden files could'nt be unhided using properties (Hidden option was greyed out), so we have to use command prompt.
Firstly, install a good antivirus (i prefer kaspersky, as it is what i have), and scan and remove the infections in the pendrive and your machine.
Then open cmd (Start>Run>cmd), and type:
"cd x:\" (where x is the drive letter for your pendrive). OR firstly "cd\" or "cd/", then type "x:\". (without quotes).
"attrib *.* -s -h /s /d" (without quotes).
Now, you will be able to see all your data.