A method for measuring thin film thickness variations of inspected wafer that includes an upper non-opaque thin film. The method including (i) scanning the wafer and obtain wafer image that includes die images each of which composed of pixels, (ii) identifying regions in a first die image and obtain first intensity measurements of the respective regions, (iii) identifying corresponding regions in a second die image and obtain second intensity measurements of the respective regions, (iv) processing the first intensity measurements and the second intensity measurements to obtain signal variations between the second intensity measurements and the first intensity measurements, whereby each calculated signal variation is indicative of thickness variation between a region in the second die and a corresponding region in the first die.