Methods and systems are described that mark and/or correct margin lines and/or other features of dental sites. In one example a three-dimensional model of a dental site is generated from intraoral scan data of the dental site, the three-dimensional model comprising a representation of a preparation tooth. An image of the preparation tooth is received or generated. Data from the image is processed using a trained machine learning model that has been trained to identify margin lines of preparation teeth, wherein the trained machine learning model outputs a probability map comprising, for each pixel in the image, a probability that the pixel depicts a margin line. The three-dimensional model of the dental site is then updated by marking the margin line on the representation of the preparation tooth based on the probability map.