For Windows, Java Console API project provides functionality to determine console size and set cursor position. Clearing the screen is trivial with that. It's a version 0.2 now so it's not exactly production ready, but it works.
Alternatively, you can simply print out some new lines via System.out.println()
. 640 should be enough for everybody :-) It's not the same as clearing screen, but for user's intents and purposes it'd do.