The present invention may include loading a diagnostic sample onto a sample stage, focusing light from an illumination source disposed on a multi-axis stage onto the diagnostic sample, collecting a portion of light reflected from a surface of the diagnostic sample utilizing a detector, wherein the illumination source and the detector are optically direct-coupled via an optical system, acquiring a set of diagnostic parameters indicative of illumination source position drift from the diagnostic sample, determining a magnitude of the illumination source position drift by comparing the acquired set of diagnostic parameters to an initial set of parameters obtained from the diagnostic sample at a previously measured alignment condition, determining a direction of the illumination source position drift; and providing illumination source position adjustment parameters configured to correct the determined magnitude and direction of the illumination source position drift to the multi-axis actuation control system of the multi-axis stage.