The current prune user function is slow and ineffective when handling a lot of users at once (50+).
For example, you want to remove all users with no posts that have been piled up during the years and reached a couple of thousand users. Trying to prune users by condition post count = 0 wont work, as it will freeze your browser for undefined amount of time, as the browser tries to render the confirmation page (with 1000+ items).
When trying to limit the amount of users it will prune, say by date, you can actually get to the confirmation page. Say 100 users was returned by the search and you confirm this. After 30 seconds or so (depending on server settings, for me it was 30 seconds), it will timeout. Checking the number of users deleted, it's usually around 40 - 50 users before it timeouts.
This makes the whole process tedious and slow, and there should be a better way to do it. If you know SQL you could try to remove all relevant users yourself in a couple of seconds, but that may or may not cause side-effects, like the one I reported here: http://tracker.phpbb.com/browse/PHPBB3-12086.