A method of compensating for motion of objects during a surgical procedure is provided. The method includes determining a pose of an anatomy of a patient; determining a pose of a surgical tool of a surgical device; defining a relationship between the pose of the anatomy and a position, an orientation, a velocity, and/or an acceleration of the surgical tool; associating the pose of the anatomy, the pose of the surgical tool, and the relationship; and updating the association in response to a motion of the anatomy and/or a motion of the surgical tool without interrupting operation of the surgical device during the surgical procedure.