A method and system is described that greatly improves the safety and efficacy of ophthalmic laser surgery. The method and system are applicable to precise operations on a target subject to movement during the procedure. The system may comprise the following elements: (1) a user interface, (2) an imaging system, which may include a surgical microscope, (3) an automated tracking system that can follow the movements of an eye, (4) a laser, (5) a diagnostic system, and (6) a fast reliable safety means, for automatically interrupting the laser firing.