The present invention provides a method for determining a position of a joint prosthesis using a computer assisted orthopedic surgery system in support of an arthroplasty surgery. The method includes attaching a first locatable element to a first bone on one side of a joint, providing a sensor having a second locatable element and moving the sensor in proximity of the joint to locate a plurality of positions of the sensor relative to the first locatable element using a tracking device. The method further includes selecting a generic model of a joint, determining the generic model in response to the plurality of positions located using the tracking device to generate a deformed model, determining a position for a joint prosthesis on the deformed model, and outputting on a display the determined position upon the deformed model.