A laser system to treat an object with a laser beam, comprising: a laser to generate the laser beam; a tomography system to generate a measurement beam and measure an optically transmissive material of the object, the object being selected from the group consisting of an eye, a fluid of a patient interface above the eye, and a calibration apparatus comprising one or more structures similar to a structure of the eye; an optical delivery system coupled to the laser and the tomography system to deliver the laser beam and the measurement beam to the object; a memory storing a look-up table, characterised by: the look-up table including values mapping object coordinate locations to values of machine controllable dimensions of the laser and of the tomography system; and a processor coupled to the laser, the tomography system, and the optical delivery system, the processor comprising a tangible medium embodying instructions to: in response to the look-up table values mapping object coordinate locations to values of machine controllable dimensions of the laser, mark the object at one or more mark locations corresponding to each of one or more target locations, the one or more target locations comprising locations of one or more of a cornea, an aqueous humor, an iris, an anterior lens capsule, a posterior lens capsule, a cortex, or a nucleus and, in response to the look-up table values mapping object coordinate locations to values of machine controllable dimensions of the tomography system, measure with the measurement beam a location for each of the one or more marks with the measurement beam, and compare the corresponding target location with the measured location for each of the one or more marks in order to determine one or more of calibration or eye position. a laser to generate the laser beam; a tomography system to generate a measurement beam and measure an optically transmissive material of the object, the object being selected from the group consisting of an eye, a fluid of a patient interface above the eye, and a calibration apparatus comprising one or more structures similar to a structure of the eye; an optical delivery system coupled to the laser and the tomography system to deliver the laser beam and the measurement beam to the object; a memory storing a look-up table, characterised by: the look-up table including values mapping object coordinate locations to values of machine controllable dimensions of the laser and of the tomography system; and a processor coupled to the laser, the tomography system, and the optical delivery system, the processor comprising a tangible medium embodying instructions to: in response to the look-up table values mapping object coordinate locations to values of machine controllable dimensions of the laser, mark the object at one or more mark locations corresponding to each of one or more target locations, the one or more target locations comprising locations of one or more of a cornea, an aqueous humor, an iris, an anterior lens capsule, a posterior lens capsule, a cortex, or a nucleus and, in response to the look-up table values mapping object coordinate locations to values of machine controllable dimensions of the tomography system, measure with the measurement beam a location for each of the one or more marks with the measurement beam, and compare the corresponding target location with the measured location for each of the one or more marks in order to determine one or more of calibration or eye position. the look-up table including values mapping object coordinate locations to values of machine controllable dimensions of the laser and of the tomography system; and a processor coupled to the laser, the tomography system, and the optical delivery system, the processor comprising a tangible medium embodying instructions to: in response to the look-up table values mapping object coordinate locations to values of machine controllable dimensions of the laser, mark the object at one or more mark locations corresponding to each of one or more target locations, the one or more target locations comprising locations of one or more of a cornea, an aqueous humor, an iris, an anterior lens capsule, a posterior lens capsule, a cortex, or a nucleus and, in response to the look-up table values mapping object coordinate locations to values of machine controllable dimensions of the tomography system, measure with the measurement beam a location for each of the one or more marks with the measurement beam, and compare the corresponding target location with the measured location for each of the one or more marks in order to determine one or more of calibration or eye position. in response to the look-up table values mapping object coordinate locations to values of machine controllable dimensions of the laser, mark the object at one or more mark locations corresponding to each of one or more target locations, the one or more target locations comprising locations of one or more of a cornea, an aqueous humor, an iris, an anterior lens capsule, a posterior lens capsule, a cortex, or a nucleus and, in response to the look-up table values mapping object coordinate locations to values of machine controllable dimensions of the tomography system, measure with the measurement beam a location for each of the one or more marks with the measurement beam, and compare the corresponding target location with the measured location for each of the one or more marks in order to determine one or more of calibration or eye position.