This invention introduces an oral-dental anatomy modeling method and an implant treatment planning system based on a full anatomy model (FAM). Dental Implant Treatment Planning systems place implants on 2D slices of DICOM files, and sometimes on 3D models of bones and remaining teeth. Because the final look and feel of implants and restorations depend on how well they go along with the remaining teeth and soft tissues, treatment planning without tissue model presents safety and aesthetics risks. A FAM consists of models for bones, teeth, soft tissues and nerves. They are created from CT and optical scans, and assembled together with model registration techniques. The tissue model is the real differentiator. A treatment planning system uses FAM as a unique reference throughout the workflow. Its implant placement, restoration preview and surgical guide design are all based on FAM.