In my application I have a wrapper over some native code, which is called via JNI bridge. This native code needs to be executed in separate thread (parallel processing). How
Since you are dealing with 3rd party code I would suggest creating a native shell application that handles calling, tracking and terminating these threads. Better yet get this 3rd party to do it for you if your licence agreement offers any kind of support.
http://java.sun.com/docs/books/jni/html/other.html