Depends on how heavy the marks are and where they are. If they aren't too heavy you may be able to sand them out without changing the shape. If they are heavier you could consider cutting out the marked area and replacing the balsa there. This isn't as big a job as it sounds, especially if you have done any building and/or repairing of planes yourself previously. An intermediate step could be to sand the area down even to the point of distorting the shape - depending on what kind of area it is - and then filling with light weight spackle and covering. Loss of strength with this method, so make sure it's someplace where you can tolerate this method. With very light color Monokote - or any similar covering - painting over the marks probably won't help much as you'll be able to see the painted areas versus the other areas underneath.