Oh I see, well there are a few different ways. My favorite way is to get a thread chaser, not a tap, and chase the threads out, use a little WD-40 or something to lube it up when you do. Next would be to use a tap to clean them out. Same thing as a chaser only it is a tap and it is designed to CUT new threads, so you can and sometimes will remove a little steel when you do it. I prefer to remove as little metal as possible, preferably none, when I chase threads. Lastly you can just run a brush on a drill motor down the threads. I have a few long handled bore brushes that are made for that stuff and you can also use rifle bore brushes, they come in stainless steel and phosphor-bronze and they will clean the internal threads just like a wire wheel cleans the outers.

Mark