A system for determining the alignment measurement of the foot and ankle is disclosed. The system uses data representative of a three dimensional scanned image of a patient's foot and ankle while the patient was applying weight on the foot. Next the system detects the three dimensional coordinates associated with at least three predetermined landmarks on the patent's foot in the scanned image. A ground plane is determined using the predetermined landmarks. A center of a talar dome is determined in the scanned data. An ankle offset lever arm id determined from the set of landmarks and center of the talar dome.
