A system and method for correcting surface height measurements for optical aberration is provided. Heights determined by an autofocus tool, which may depend on surface feature angles in a focus region of interest (ROI) and on the ROI location in the field of view, are corrected based on a novel error calibration. Error calibration data includes height corrections for different feature angles in images, and for multiple locations in a field of view. Height corrections are determined by weighting and combining the angle dependent error calibration data, e.g., based on a gradient (edge) angle distribution determined in the ROIs. When Z-heights are determined for multiple ROIs in a field of view, storage of image data from particular images of a global image stack may be efficiently controlled based on determining early in processing whether a particular image is a sufficiently focused "near-peak" focused image or not.