A computer-assisted imaging and localization system assists the physician in positioning surgical effecters, such as implants, tools and instruments, within a surgical site in a patient's body. The system displays overlapping images—one image of the surgical site with the patient's anatomy and another image showing the surgical effecter(s). The overlapping image of the surgical effecter(s) is moved over the static image of the anatomy as the implant/instrument is moved. The movement of the surgical effecter(s) is determined in a three-dimensional coordinate system at a home base location in the patient's anatomy, which home base can be moved during the procedure without interrupting the displays of the overlapping images.