Abstract: A method of forming a procedure plan includes arranging a tracking arm distal end in communication with a reference location (RL) about a site or an object received thereat (S/O), the RL disposed in relation to the tracking arm in a 3D space. Physical points about the S/O are each contacted with an end effector of a procedure tool engaged with a robot arm disposed in known relation to the tracking arm, and locations thereof concurrently determined in the 3D space. A reference frame (RF) is formed in the 3D space, relative to the RL, from the locations of the physical points, and includes a location of the S/O within the RF. A plan is formed for an end effector procedure on the S/O, within the RF and relative to the RL, including a route traversed by the end effector to and from the S/O and during the procedure.