may be you could using timer, it has schedule method to define how long the
thread should run.

this depends on what you are trying to do.
If your application creates their own threads (to do some
parallel processing e.g.) then you can of course kill
this thread  inside your application (since you are
the owner).
If you are talking about threads in a linux/unix world then
you take a look at the Runtime class in Java which gives
you the ability to call "system commands" like cp, rm, kill  and so on.