Well, the way that would involve least harm is to not "do a wash" (as we call it where I live) on used filters at all. If you're worried about leaving some of the dope trapped in the filter, do a wash on them immediately, by adding some more water to the cooker, drawing it up through the filter to get every last bit of dope out of there before you do your shot. That will also reduce the temptation to re-use them.
If you are one of those people who deliberately saves them up so you can do a wash on a bunch of them when you're junksick and have no money, well I can understand that, as unwise as it is. What I started doing instead was saving a very tiny bit of dry heroin every time I did a shot, so that would be my way to gradually save up a little stash for emergencies. If you get everything out of your filters when you use them, and you save a little bit like this, it's less risky, less wasteful, and you don't have to mess around with 30 filters and not knowing exactly how much dope you'll be able to get out of them etc when you're sick and broke.
If you're still going to do filter shots anyway, here's what I would advise to try to reduce risk (and make the most of it):
- allow them to dry completely as opposed to storing them wet (this will reduce the potential for bacterial growth)
- store them in something clean and dry
- put them in a cooker with plenty of water, you may need significantly more water than you'd need for a normal shot, depending on how many filters you're using at once
- apply a little heat
- try to suck as much liquid as you can out of the filters with a syringe
- add more water
- again draw up as much water out of the filters as possible
- squirt the solution into a clean cooker
- apply heat (this will kill off some bacteria/viruses but not all!)
- put a clean filter into the solution and draw up into a clean syringe
- add a tiny bit more water and draw up again to make sure you got it all out of this last filter
