1. A method of calibrating an scanner head of an atomic force microscopy (AFM) machine comprising: loading a calibration sample into the AFM machine; scanning deep features formed in the sample with an AFM tip attached to the scanner head along a first line in a first direction; determining a first tip angle measurement for the AFM tip relative to the sample along the first line for at least two of the deep features scanned along the first line; scanning deep features formed in the sample with the AFM tip along a second line in a second direction, wherein the second direction differs from the first direction; determining a second tip angle measurement for the AFM tip relative to the sample along the second line for at least two of the deep features scanned along the second line; determining a first function corresponding to the first tip angle measurements versus position along the first line; determining a second function corresponding to the second tip angle measurements versus position along the second line; and storing the first and second functions as the arc functions for the scanner head.