Maybe a little rethink about how you implement the threads and switch to Parallel::Forker? I talked about it before ( here ), and it sounds like you need a similar upgrade in your thread control as OP did there.

Alternately, if you keep track of the pid, you can manually kill it, but i am not sure how safe / easy that would be (and it depends on you OS etc...). See kill and try super searching.

Update Added second paragraph.