By taking a picture when the angle of incident electrons is normal to the object and comparing it to a picture taken at a 20 degree angle, the parallax that occurs can be used to calculate the depth of the hole at different points.

This is only possible when there are identifiable features inside the holes. The diameter of this hole was exceptionally large because the etching bath was too hot during this particular etch. Large holes have identifiable features, but normal size holes do not.