1. A method for generating a modified virtual model of a physical structure, comprising: (A) displaying an image of a first virtual model on a display operatively connected to a computer system, wherein the first virtual model is generated from first 3D scan data of the physical structure, and wherein said first virtual model fails to properly represent a first physical part of the physical structure; (B) receiving user input identifying at least a portion of the first virtual model that is desired to be modified, wherein the user input is generated by user interaction with the image on the display; (C) receiving a second virtual model of the physical structure with the computer system, the second virtual model generated from second 3D scan data of the physical structure; and (D) modifying the first virtual model with the computer system by replacing at least said identified portion of the first virtual model with a corresponding portion of the second virtual model, thereby generating the modified virtual model.