Missing folders/files from my wd hard drive from virus?

heres the story. I received the "windows vista restore" virus on my laptop, its been taking away all the shortcuts and such but no information is being deleted. I went to my desktop with my external hd to download a program to stop the virus and when i plugged my external hd in to my laptop to install it, everything was wiped from it. Its like the files are hidden. It Still says the same amount of space is being used up so I know they are not deleted. any advice? I'm running windows 7 and if there is any info on getting rid of the virus as well that would be helpful.