Speaking from the experience of having co-developed something similar to Mimics some twenty+ years ago: It is often much easier to manually change the track of a contour instead ot modifying the pixel structure the contour is based on.
 What speaks against something like this: Instead of marking new pixels to be added or subtracted to a mask (mostly also leading to a lego-brick-like surface) it ist much easier to edit a contour. The user interface could be very simple: Click on two points that mark the segment that you want to alter. Start and end could alway be oriented clockwise, as seen from the user, thus avoiding ambiguities.
Or mark two points and then mark the segment that you want to alter. Since all contours a re circular with some overtones in their spectrum, there are always two choices of contour parts to be edited. Choose the one you want.
Then "draw"a new contour segment that will replace the marked vector chain. When you hit the end point, the contour is automatically closed again.
Any comment from Materialise?  I can tell you: It works. You are welcome to take this as a free advice :).
Cheers,
Ulli