1. A computer assisted surgery system for positioning a surgical instrument relative to a surgical implant within a patient's body, said system comprising: a surgical instrument defining a trajectory; a surgical implant with one or more holes; a localizing device for measuring the pose of the surgical instrument and the pose of the surgical implant; means for acquiring x-ray images of the surgical implant; means for calculating an adjusted pose for the surgical implant, said means for calculating the adjusted pose based on information developed from the x-ray images; and means for displaying a graphic representation of the trajectory relative to a graphic representation of the surgical implant, based on the measured pose of the surgical instrument and the adjusted pose of the surgical implant; wherein the adjusted pose of the implant compensates for deformation of the implant or inaccuracies in localization, so as to assist a surgeon in aligning the trajectory of the surgical instrument with the holes in the surgical implant.