Lamella alignment based on a reconstructed volume

An apparatus comprising:

• a focused ion beam column coupled to provide an ion beam along an optical axis;
• an electron beam column coupled to provide an electron beam;
• and
• a controller coupled to or including non-transitory memory including code that, when executed by the controller, causes the apparatus to;
• form, using a combination of the ion beam and the electron beam, a reconstructed volume of a portion of a sample, the sample including a plurality of structures, and the reconstructed volume including a portion of the plurality of structures;
• perform, over a range of angles, a mathematical transform on each plane of a plurality of planes of the reconstructed volume;
• and
• based on the mathematical transform on each plane of the plurality of planes, determine a target orientation of the sample within the range of angles, wherein the target orientation aligns the plurality of structures parallel to an optical axis of a charged particle beam.