Microsoft's versioning for .net is a little screwy...
.Net 2.0 was originally released around the end of 2005.
.Net 3.0 was released around the end of 2006, but uses the CLR of .Net 2.0. .Net 3.0 adds Windows Presentation Foundation (WPF), Windows Communication Foundation (WCF), Windows Workflow Foundation (WF) and Windows CardSpace (WCS).
.Net 3.5 was released the end of 2007, and also uses the .Net 2.0 CLR. .Net 3.5 and 3.5 SP1 add things like Linq, Ajax, Entity Framework etc.
Since 3.0 builds on 2.0 and 3.5 builds on 2.0 and 3.0, you can't uninstall 2.0 and 3.0 if you are trying to keeping 3.5. You could uninstall 3.5 and 3.0 and run just 2.0 SP 2, but you're probably going to hit something sooner or later that requires either 3.0 or 3.5.
If you have 1.0 or 1.1 installed, I'd definitely uninstall those first.