A method and a dental implant treatment planning and surgical guide design system based on a full anatomy model (FAM). A FAM consists of models for bones, teeth, and nerves, and a virtual stone model. A virtual stone model is not only a surface model of the soft tissue and tooth surfaces of a patient, but also a color map of tissue thickness data. It also contains the insert direction of a surgical guide. The treatment planning and surgical guide system uses the full anatomy model as a unique reference throughout the workflow. Its implant placement, restoration preview and surgical guide design are all based on the anatomy model.