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I recently got a CD from a magazine. (Maximum PC) (Note : The CD has a lot of setup programs on it.) I used it, and it worked flawlessly.No problems. I then put it up. Today, I got it out,started a program on the CD, and got infected with Win32.Virut.W (Symantec). (I still have absolutely no idea how it got on the CD). ( I then disabled autorun on my computer)I removed it easily, and then later, started two different .exe setup programs. They both were infected. I ran Malwarebytes Anti Malware and it removed Win32.Virut.W again, and a worm it dropped (Worm.Autorun.B.) ( I haven't touched the CD since) I then scanned the CD with Malwarebytes Anti Mal ware , and Iobit Security 360. They both didn't find anything. (Even though clearly, the virus has infected several and probably all of the .exe files.)

So,
How can I disinfect my CD?
How did it get on my CD in the first place?

Maybe it's an false positive.
I'm not the best guy to help you out with this, but I've seen such posts from time to time.
Check out the Homepage of the Magazine for some information about it and also their forum would be a lot better to ask this.

I'm not sure if it's a false positive, or if it's not. It does come from Maximum PC which is quite odd. Symantec is also a very sensitive AV, which I've witnessed. If it's opening .exe's that contain more viruses, then that's not good.

Its not a false positive. I started some of the programs from the CD and they infected me with Win32.Virut.W. After I quarantined the files, I scanned it with Virus total,and went with Symantec's alias.
Here are the links to the Virus Total scans :
http://www.virustotal.com/analisis/3f157...1260656775
http://www.virustotal.com/analisis/a62b1...1260660433

http://www.virustotal.com/analisis/a62b1...1260660433

I scanned the CD with Malwarebytes,and It couldn't find anything. Does anyone know a program that I could use to scan the CD and remove the infections from the .exe files?

You might want to use a good anti virus software for that. Mabey Avast. I use Avast and it finds everything that is dangerous for your computer. I realy recomend that anti virus software.

A good virus software to use is ESET and its possible you already had the virus and got rid of it ,but then it jumped onto the CD and then when you put it back in it started back up.