A method of automatically adjusting lighting conditions improves the results of points from focus (PFF) 3D reconstruction. Multiple lighting levels are automatically found based on brightness criteria and an image stack is taken at each lighting level. In some embodiments, the number of light levels and their respective light settings may be determined based on trial exposure images acquired at a single global focus height which is a best height for an entire region of interest, rather than the best focus height for just the darkest or brightest image pixels in a region of interest. The results of 3D reconstruction at each selected light level are combined using a Z-height quality metric. In one embodiment, the PFF data point Z-height value that is to be associated with an X-Y location is selected based on that PFF data point having the best corresponding Z-height quality metric value at that X-Y location.