Assuming that "conditioning" means you carbonate the beer naturally as opposed to force carbonation, then you most definitely do not want to filter prior to conditioning.
If you force carbonate then it doesn't much matter.
With proper aging the cloudiness will be minimal, and even if you've got a lot of yeast in the brew about the worst it will do to you is give you gas.
Unless there is a real need for a crystal clear brew, like selling it, I don't know why you would need to filter in the first place.