An apparatus and method are provided for performing ocular laser surgery using a patient interface having a posterior contact surface that may include surface irregularities that were generated during manufacturing of the patient interface. A beam delivery system having a focusing lens, scanning subsystem and adaptive optic (e.g. deformable mirror) is provided for guiding the surgical laser beam through the patient interface and to a desired focal spot location. An optical detector generates image data representing the posterior patient interface surface which is then processed by a computer system to identify surface irregularities by comparing the image data to a reference surface or axis. In particular, a surface irregularity can be identified as having a z-axis component; a tilt component and a surface profile component. Each irregularity component can be compensated separately by sending an adjustment signal to one of the beam delivery system components.