A surgical apparatus includes a surgical device, configured to be manipulated by a user to perform a procedure on a patient, and a computer system. The computer system is programmed to create a representation of an anatomy of a patient; to associate the anatomy and a surgical device with the representation of the anatomy; to manipulate the surgical device to perform a procedure on a patient by moving a portion of the surgical device in a region of the anatomy; to control the surgical device to provide at least one of haptic guidance and a limit on manipulation of the surgical device, based on a relationship between the representation of the anatomy and at least one of a position, an orientation, a velocity, and an acceleration of a portion of the surgical device; and to adjust the representation of the anatomy in response to movement of the anatomy during the procedure.