In a method of generating a virtual 3D model of a dental site, scan data comprising a plurality of images of a dental site is received during an intraoral scan. An analysis of an image is performed. A representation of a reference object with known properties is identified in the image based on the analysis. A virtual 3D model of the dental site is generated based on the plurality of images. The image and/or the virtual 3D model of the dental site is modified by adding additional data about the reference object to the intraoral image and/or the virtual 3D model based on the one or more known properties of the reference object. If the image is modified, it may be modified prior to generation of the virtual 3D model, and the virtual 3D model may be generated using the modified image.
