Actually, I do use flush cutters and cut a couple of mm away from the part. Then I sand it down. Also, I use a grinder which is the most expedient way. Sawing through resin sprues and resultant trimming is the most reliable method. Use a ladies' emery board or a hobby sanding stick instead.
Experience is the best teacher, but that was a VERY expensive lesson.
In these cases, make sure you have Gunze Sangyo's Mr. Surfacer handy. It will fill in these microscopic marks. An example of how well this works, I use 400 grit sandpaper to do the rough sanding. Then I graduate to 600-800 grit for the final polishing. However, the 400 grit will leave some rather deep scratch marks.