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Severe malformations of the midface such as maxillary or mandibular deformity can be treated by distraction and reformation of skull bones. During an operation, the appropriate bony part of the mid-face is separated from the rest of the skull (osteotomy), slowly moved into the ideal position by way of a distraction device. In the current clinical practice, planning for orthognathic surgery was based on CT scans. While CT images inefficient for helping the surgeons in treatment and surgical planning so we need a tool that helps the physicians and surgeons in the treatment planning in order to give the true decision. The advantage of the Computer aided treatment planning is to provide an integrated three-dimensional planning and simulation environment for orthodontic treatment, to help orthodontists to accurately visualize 3D model for the patient and to prepare for the treatment plan before the treatment begins. There were many software packages that apply 3D visualization and segmentation but in a manual way not in an automatic segmentation like our software.