Measuring a height profile of a hole formed in non-conductive region

A system, computer program product and a method for measuring a hole. The method may include charging a vicinity of the hole having a nanometric width; obtaining, multiple electron images of the hole; wherein each electron image is formed by sensing electrons of an electron energy that exceeds an electron energy threshold that is associated with the electron image; wherein electron energy thresholds associated with different electron images of the multiple electron images differ from each other; receiving or generating a mapping between height values and the electron energy thresholds; processing the multiple electron images to provide hole measurements; and generating three dimensional measurements of the hole based on the mapping and the hole measurements.