It only zaps threads that have not had any post or reply within 60 days. So a thread with an original topic start date of 6/15/98, but has a current reply of 3/31/01 will not be pruned, for example.
Keep in mind that before the prune is executed it will show you a list of all the topics it is going to delete. You are then able to check older threads you still want to keep on that screen which will cause the prune to skip them.