There are different types of machines. I personally own a T Tech machine and know the people who first developed it and built the first generation. I used it on my 96 Tahoe and it went 204k before i traded it in and the 4l60e was still shifting perfectly. This is considered a fluid exchanger. The fluid is moved by the trans pump so yes the vehicle is running. The benefit of this is that the fluid is forced back in with the same pressure that is normally present and as the old fluid is forced into the machine the new fluid is forced back into the machine so it never is run low. Thats how the valve body and converter are cleaned. A flush machine can be one with a seperate pump that a tech dials in to match the pressure out of the trans which leaves you depending on their diligence. As far as the filter goes, i changed it every 30-40k and i always felt if you kept the fluid clean the filter wouldnt need to be changed as often.