A laser system calibration method and system are provided. In some methods, a calibration plate may be used to calibrate a video camera of the laser system. The video camera pixel locations may be mapped to the physical space. A xy-scan device of the laser system may be calibrated by defining control parameters for actuating components of the xy-scan device to scan a beam to a series of locations. Optionally, the beam may be scanned to a series of locations on a fluorescent plate. The video camera may be used to capture reflected light from the fluorescent plate. The xy-scan device may then be calibrated by mapping the xy-scan device control parameters to physical locations. A desired z-depth focus may be determined by defining control parameters for focusing a beam to different depths. The video camera or a confocal detector may be used to detect the scanned depths.
