I've found information on uninstalling most of the .NET Frameworks using Msizap but having trouble uninstalling .NET 3.5 Framework. Some DLLs got corrupted from a recent virus attack and I'm having trouble running some of my .NET 1.1 applications that make use of the entire .NET library. Creating and running a test .NET 1.1 application of just a messagebox seems to work just fine but beyond that it's hosed.
You could try the dot net clean up tool. I had to use it once and it worked very well.
If your antivirus software can't clean it then the recommended solution is a clean re-install of everything rather than trying to find and fix individual parts. You never know where things may be hiding.