I presume the scratches came from the cutting process? Or were they from sanding after the putty dried? In either case, you need to sand some more to get rid of the scratches. Start with a coarser grain and then go step by step thru the finer grains. It may still look cloudy, but once you prime or paint, it wont' show. If it bothers you before the painting, you can use a product like Novus plastic polish, its a paste that will create a very smooth surface.