A system and method for providing magnetic based navigation in dental implant surgery is disclosed. According to one embodiment, a surgical navigation system comprises a custom piece that is made to fit in a patients anatomy and comprises a first magnetic component. The surgical navigation system further comprises an instrument assembly comprising a drill bit and a second magnetic component. A processing unit receives and displays a first position and orientation data from the first magnetic component with respect to a second position and orientation data from the second magnetic component to track the movement of the first magnetic component with respect to the second magnetic component.
