that tool will only remove versions of .NET that have been installed as updates. It won't touch the versions included in the operating system. Hence the need to remove the updates using the tool, use SFC to hopefully repair the versions included with the OS, and then update.
There is NO way to remove those versions included in the OS -all you can hope to do is repair, and if that fails then its a rebuild -or repair installation
When I say it won't affect your programs - it won't, as long as the .NET is reinstalled after. The programs won't be affected - but their ability to run maybe, hence the need to reinstall. However when you get down to it, very few non-internet routines need .NET in any form to run
As to the catroot folders theres all kinds of stuff in there - and deleting should only be done as a last resort. You need to disable BITS and Windows update services first, and then re-enable once done. You've probably got multiple iterations of then due to past system restores