Abstract: A method and apparatus associated with an atomic force microscope (AFM) to more accurately measure the height of a microscopic feature in a substrate, particularly one having a sloping face. The probe tip is sequentially positioned at a number of vertical positions approaching the surface being probed. At each vertical position, a vertical force encountered by the probe tip is measured, and the measured force is stored in a memory together with its corresponding vertical position. When the measured force exceeds a threshold force, the downward movement is stopped, and the accumulated force and position data are analyzed. A controller fits the data to two curves, for example, two linear relationships in force vs. height. One curve is associated with the lower forces away from the surface, the other curve with the higher forces after initial engagement with the surface. The intersection of the two curves gives the height of the feature in the surface.