1. A method for cross-sectioning a sample with a preset thickness, comprising: providing a sample having x, y and z dimensions with at least first and second line structures on a surface of the sample defined by the z-x plane, the at least first and second line structures each extending from the x-y plane at known angles and having ends electronically detectable on a first from a cross-section surface of the sample defined by the x-y plane; exposing a second cross-section surface defined by the x-y plane with a material removal tool, where an x dimension distance between ends of the at least first and second line structures exposed in each cross-sectioned surface changes along the z-dimension; electronically calculating a first distance in the z-dimension between the first cross-section surface and the second cross-section surface based on a change in the x dimension distance and the angles; automatically adjusting parameters to advance the material removal tool in the z dimension for exposing a third cross-section surface at a second distance in the z dimension from the second cross-section surface that is closer to the preset thickness than the first distance.