Instrumentation, systems, and processes for tracking anatomy, instrumentation, trial implants, implants, and references, and rendering images and data related to them in connection with surgical operations, for example total knee arthroplasties (“TKA”). These instrumentation, systems, and processes are accomplished by using a computer to intraoperatively obtain images of body parts and to register, navigate, and track surgical instruments. Disclosed in this document are also alignment modules and other structures and processes which allow for coarse and fine alignment of instrumentation and other devices relative to bone for use in connection with the tracking systems of the present invention.