A laser eye surgery system, comprising: a laser to generate a laser beam; a spatial measurement system to generate a measurement beam and measure a spatial disposition of an eye; a processor 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; map the spatial model from the eye coordinate reference system to a machine coordinate reference system; receive a rotation angle of a corneal incision relative to a reference axis of the machine coordinate reference system; determine a laser fragmentation pattern based on a plurality of laser fragmentation parameters, characterised in that the tangible medium further embodies instructions to: determine a first rotation angle based on the rotation angle of the corneal incision and a rotation angle of the laser fragmentation pattern relative to the reference axis of the machine coordinate reference system; rotate the spatial model by a negative of the first rotation angle; and rotate the laser fragmentation pattern and the spatial model by the 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. a laser to generate a laser beam; a spatial measurement system to generate a measurement beam and measure a spatial disposition of an eye; a processor 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; map the spatial model from the eye coordinate reference system to a machine coordinate reference system; receive a rotation angle of a corneal incision relative to a reference axis of the machine coordinate reference system; determine a laser fragmentation pattern based on a plurality of laser fragmentation parameters, determine a spatial model of the eye in an eye coordinate reference system based on the measurement beam; map the spatial model from the eye coordinate reference system to a machine coordinate reference system; receive a rotation angle of a corneal incision relative to a reference axis of the machine coordinate reference system; determine a laser fragmentation pattern based on a plurality of laser fragmentation parameters, characterised in that the tangible medium further embodies instructions to: determine a first rotation angle based on the rotation angle of the corneal incision and a rotation angle of the laser fragmentation pattern relative to the reference axis of the machine coordinate reference system; rotate the spatial model by a negative of the first rotation angle; and rotate the laser fragmentation pattern and the spatial model by the 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. determine a first rotation angle based on the rotation angle of the corneal incision and a rotation angle of the laser fragmentation pattern relative to the reference axis of the machine coordinate reference system; rotate the spatial model by a negative of the first rotation angle; and rotate the laser fragmentation pattern and the spatial model by the 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.