A system for generating a 3D model of a surgical site includes a 3D endoscope and a computing device coupled to the 3D endoscope. The 3D endoscope includes a scanner for scanning a surface of a surgical site and a camera source for generating images of the surgical site. A 3D model of the surgical site, including objects therein, is generated using scan data and image data. The 3D model is updated by detecting a change in the surgical site, isolating a region of the surgical site where the change is detected, generating second scan data by scanning the surface of the isolated region, and updating the 3D model generated using the second scan data of the surface of the isolated region.
