I couldn't find anything in the V3 reference which will explicitly clear the overlays created on the map and I could't find any code samples which do this either.
I think that it is important to point out the V3 API is a very early developer release and contains only a very basic set of features. It is quite possible that they simply haven't got to this functionality yet. If you are working on a live system, I suggest you stick with V2 until V3 is more mature.
There is a post on the developer group which asks the question about how the API should be used with a very useful answer from the V3 product manager:
Misconception about v3 Options
EDIT:
OK, it seems like this functionality is missing from the API deliberately in order to keep it lightweight. You should keep track of your overlay objects yourself and call:
object.set_map(null);
to remove them.