The invention generally pertains to a combination of a haptic device with a computer-assisted surgery system. The haptic device may be used as an input device, allowing information to pass from the user to the computer-assisted surgery system, and providing functionality similar to common user interface devices, such as a mouse or any other input device. When used as an input device, it may be used for defining anatomical reference geometry, manipulating the position and/or orientation of virtual implants, manipulating the position and/or orientation of surgical approach trajectories, manipulating the positions and/or orientation of bone resections, and the selection or placement of any other anatomical or surgical feature.