Re-install OS, Trojan

Hi guys I believe I have a serious virus on my PC. Internet is slow but I can ping out, and I am getting a lot of pop-ups and redirection when I browse internet. So I have a 320 GB hard drive and that is where my OS is installed, and I have another 500GB HD and that is where I have my movies, games and music. My question is if I format my 320 GB HD and re-install my OS is my 500HD gonna be affected? I don't want to lose my data!!!!!Thanks.
 
2 more questions. I have to re-install the same OS version right, like Vista 32 for example? Also what if all those movies and files I haved moved from 320 GB HD to 500GB HD, could it be possible that those files may have viruses and transfer to the newly installed HD? Thanks.
 
I can't tell you where the virus is, but it is possible it's embedded in an exe or rar some where, have you tried dealing with the virus yet?
 
The virus will be in the OS, it will be in the OS itself.

We can help you try and get rid of the virus and save you reinstalling....
 
OK so I installed Vista 64 bit in the 320GB HD and now I have "Program Files" and "Program Files(x86)". "Program Files(x86)" is my new install. I can't delete "Program Files". What can I do to remove it?
 
I believe both of them are new. Program files is for 64bit and Program files(x86) is for 32bit I believe.
 
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