A system for additive manufacturing machine energy beam alignment error compensation includes, a calibration table having x-y planar offsets to correct laser alignment errors representing energy beam positional offsets between beam-steering commanded energy beam locations and fiducial marks generated on a burn-paper, a recoater mechanism that distributes successive layers of powder, one or more sensors monitoring the powderbed surface proximal to the beam scan unit, and a processor unit configured to perform a method. The method including collecting sensor data representing height variations across at least a portion of the powderbed surface, deriving dimensional data from the collected data, analyzing the dimensional data to determine a distribution of differences between the powderbed surface and a reference plane containing the burn-paper when the fiducial marks were generated, and calculating z-axis calibration offset points for inclusion in the calibration table x-y planar offsets. A method and a non-transitory medium are also disclosed.