1. A computer system for dental implant treatment planning and surgical guide design based on a full anatomy model, comprising: A. a computer hardware system with an operating system, B. an interactive computer software that is saved to a non-transitory computer readable medium, which, generates images and graphics shown on a display of the computer, and performs the treatment planning simulation and surgical guide design, wherein: i. the full anatomy model comprising, bone, teeth, and nerve model as well as a virtual stone model is created from CT scans and/or optical scans of a patient, ii. implant treatment planning is performed with said full anatomy model, iii. the surgical guide is designed based on said anatomy model. C. a geometric modeling system provided to create virtual stone model from CT scan of a radiographic guide, comprising both anatomy surface data and information for surgical guide design, wherein the virtual stone model is created by: i. registering the radiographic guide with the bone structure, ii. creating the surface model of the guide by contouring the CT scan of the radio graphic guide, or other imaging technique, iii. defining a model view direction as an extraction/insertion direction along which the radiographic guide can be put into or pulled out of the patient's mouth, iv. splitting the guide model into two portions, v. completing the polygonal modeling technique to fill holes on the model from undercuts, vi. for fully edentulous case go to step vii and for partially edentulous case: 1) output the result as a tissue-tooth model, 2)a distance map between the tissue-tooth model and the bone tooth model is evaluated to create a triangulated surface model, a vertex is represented as its coordinate and a scalar value and in order to represent the distance map and the scalar value is set to the distance between an extracted model vertex and the bone-tooth model, 3) identify tooth areas through filtering distance map wherein if a vertex is on the tooth area its value should be close to zero and all the vertices and their triangle can then be removed from the model, vii. the resulted output is the surface model of the soft tissue, viii. the model is offset or extruded towards the bone structure, ix. the result is trimmed by the bone-tooth model; D. whereby the system tools for implant planning, virtual restoration preview and surgical guide design are all based on the virtual stone model as a common reference.