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 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 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.