If recessed marks, I fill with putty and then file smooth. If protruding, I file them with needle files. I like the needle files for this work because it takes off plastic as fast as coarse sandpaper, but leaves very fine scratches like quite fine wet or dry paper. Also, files can be cleaned many times, so I find them cheaper than sandpaper.
BTW, there is a Techniques forum in the FSM hierarchy where seam filling and ejector marks are a frequent thread.