A patient positioning system for use with a radiation therapy system that monitors the location of fixed and movable components and pre-plans movement of the movable components so as to inhibit movement if a collision would be indicated. The positioning system can also coordinate movement of multiple movable components for reduced overall latency in registering a patient. The positioning system includes external measurement devices which measure the location and orientation of objects, including components of the radiation therapy system, in space and can also monitor for intrusion into the active area of the therapy system by personnel or foreign objects to improve operational safety of the radiation therapy system.