Are all mods modfoldered?

[Ferret]

Most of them don't, it should tell you in the mod description and if it doesn't you can contact a member of the team and ask. The popular ones all do.

edit:should make that clearer, I meant most of them do use the mod folders and so do not affect the vanilla game, though why you would want to go back to vanilla after playing an improved mod I don't know

[I Am Herenow]

It's just a matter of copying the vanilla directory for every mod, or not doing so :)