"Microsoft.net" was a marketing name for a set of concepts, now fallen into disuse.
I think you might be referring to the .net runtime systems, which are used by all sorts of things, including bits of the operating system. Yes it's possible that malware could be written in a .net language and require the CLR, but it's not the most obvious way to choose to do it!
Removing the .net runtimes from your machine, if you can manage to achieve this, will likely cripple all sorts of things fairly seriously.