A laser eye surgery system includes a laser to generate a laser beam. A spatial measurement system generates a measurement beam and measure a spatial disposition of an eye. A processor is coupled to the laser and the spatial measurement system, the processor comprising a tangible medium embodying instructions to determine a spatial model of the eye in an eye coordinate reference system based on the measurement beam. The spatial model is mapped from the eye coordinate reference system to a machine coordinate reference system. A laser fragmentation pattern is determined based on a plurality of laser fragmentation parameters. The laser fragmentation pattern and the spatial model is rotated by a first rotation angle such that the spatial model is aligned with the reference axis of the machine coordinate reference system and the rotated laser fragmentation pattern is aligned with the corneal incision.