In embodiments, a processing device generates a three-dimensional model of a dental site from scan data, the three-dimensional model comprising a representation of a tooth, wherein a portion of the three-dimensional model comprises an interfering surface that obscures a portion of the tooth. The processing device receives or generates an image of the tooth, wherein the image depicts the interfering surface. The processing device processes the image to generate a modified image, wherein the portion of the tooth that was obscured by the interfering surface in the image is shown in the modified image. The processing device updates the three-dimensional model of the dental site by replacing, using the modified image, the portion of the three-dimensional model that comprises the interfering surface that obscures the portion of the tooth, wherein the portion of the tooth that was obscured in the three-dimensional model is shown in an updated three-dimensional model.