I wrap a piece of tape all the way around the steerer tube first. If I did not get the tape on perpendicular, I know that right away, remove tape and start over. Then as I cut I just keep making sure I see if I am cutting along the edge of the tape. And of course before I start cutting, I mark which side of the tape to cut so that I do not accidentally make it an inch shorter than I wanted it. A few mm off and it is not a crisis.
If I already have the star nut in the steerer tube, push that down to where I want it first before I get out the hacksaw.
If you want to be obsessive about a perfect right angle, use a file later. But it never hurts to put a 5mm or 10mm spacer above your stem.