I’m waiting for my thread mic to arrive so I can really give this a go!
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Yes that is how it is done, the file gets rid of the sliver threads.Most of the machinists I've seen will run a file over the threads to flatten them a bit as a final touch. I don't know if that is official or just what I've seen and heard. I think you can be sure that if you need to cut some threads they are going to work and fit properly.
Roy