IF you want to remove scratches there is only one way to do it, but it won't prevent new ones from emerging. First, you need to remove all wax and dirt from surface of the pipe. Best is to dump cloth in 92% isopropyl alco and gently clean your pipe. next to do is to sand pipe with some fine sand paper, i usually start with 800, then go up till i get to 4000, and after that i start polishing it with polishing pads. After that you need to rewax it, but it needs to be "boiled" in molten bees wax for 8-12 mins (from personal experience). Excess was can be removed with hair dryer, just be careful not to overheat pipe with it. It should be as good as new after that, it will only color during the process (if you use yellow, unrefined bees wax it will color a lot, but some of the color will disappear after time).
As i said, this can remove scratches, but it wont prevent new scratches. As much wax you put on pipe, it wont prevent scratches, it will only prevent cracking from smoking or dropping it. If you won't wear gloves, i strongly recommend you not to do all of the above since its a bit time consuming with a mild posibility for pipe damaging.
I do this to my meers every couple of years, but i don't fuss over scratches and dings, they give pipes some character, imo.
From my point of view, worrying about those will only make you not enjoy smoking as much as you would otherwise since, again imo, there is no way to avoid them. And more you try to avoid them, more they will annoy you when they appear (and they will).
So, for conclusion, just enjoy smoking. Cheers, mate!