Abstract: A method and apparatus for a computer assisted surgery (CAS) system using alternative energy tissue and bone alteration technology. The CAS system utilizes alternative energy technology which is a directed to a surgical instrument including an alteration or cutting tip. The tip may be in contact with the tissue or bone, or, alternatively, the tip may be distant from the tissue or bone and the energy is projected to the desired cut or alteration site. The CAS system recognizes the location of the tip relative to a desired alteration location or area and de-energizes or varies the energy level when the tip moves away from or out of the predetermined alteration location or path. The CAS system provides a method for altering or resecting bone, for example, in preparation for a prosthetic implant, or a method for altering tissue, for example, cauterizing blood vessels or bonding ligaments to bones.