Microscopy imaging method and system

A method for removing material from a sample to provide a section of the sample in a charged particle beam (CPB) system having at least one charged particle beam each being controllable in position, comprising:

• providing a sample having x, y and z dimensions with first and second linear fiducials each having ends electronically detectable on a front cross-section surface of the sample defined by the x-y plane and each extending from the front cross-section surface in a direction having the z-dimension component at known angles relative to the x-y surface;
• setting a target distance m from the front cross-section surface in the z-dimension, where m is a real number;
• setting a slice distance of n, where n<m and n is a real number;
• scanning the cross-section surface to obtain a slice image thereof by an imaging system;
• iteratively executing the steps of
• a. exposing a subsequent cross-section surface defined by the x-y plane with a material removal tool to the slice distance of n, and where an x dimension distance between ends of the first and second linear fiducials exposed in each subsequent cross-sectioned surface changes along the z-dimension;
• b. scanning the subsequent cross-section surface to obtain a subsequent slice image thereof by the imaging system,
• c. electronically calculating an actual slice distance in the z-dimension between a previous cross-section surface and the subsequent cross-section surface based on a change in the x dimension distance and the angles;
• d. aggregating the actual slice distances and stopping the iterative execution of steps a-c when the aggregated actual slice distances is approximately the target distance m;
• and,
• e. automatically adjusting parameters to advance the material removal tool in the z dimension for exposing a new cross-section surface at a distance in the z dimension from the subsequent cross-section surface that is closer to the slice distance n.