A surgical implant planning computer is connectable to a fluoroscopy imager, a marker tracking camera, and a robot having a robot base coupled to a robot arm that is movable by motors relative to the robot base. Operations include performing a registration setup mode that determines occurrence of a first condition indicating the marker tracking camera can observe to track reflective markers that are on a fluoroscopy registration fixture of the fluoroscopy imager, and determines occurrence of a second condition indicating the marker tracking camera can observe to track dynamic reference base markers attached to the robot arm and/or an end-effector connected to the robot arm. While both of the first and second conditions occur, operations are allowed to be performed to obtain a first intra-operative fluoroscopic image of a patient along a first plane and to obtain a second intra-operative fluoroscopic image of the patient along a second plane that is orthogonal to the first plane.