| CPC G06T 7/74 (2017.01) [G06T 7/33 (2017.01); G06T 7/55 (2017.01); G06T 7/66 (2017.01); G06T 17/10 (2013.01); H01J 37/20 (2013.01); H01J 37/222 (2013.01); H01J 37/28 (2013.01); G06T 2207/10061 (2013.01); G06T 2207/20108 (2013.01); G06T 2207/30148 (2013.01); G06T 2210/56 (2013.01); H01J 2237/20292 (2013.01); H01J 2237/31745 (2013.01); H10B 41/27 (2023.02); H10B 43/27 (2023.02)] | 17 Claims |

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14. A charged particle microscope system, the charged particle microscope system comprising:
a sample holder of a charged particle microscope configured to hold a sample;
an electron beam source of the charged particle microscope configured to emit an electron beam toward the sample;
an electron beam column of the charged particle microscope configured to direct the electron beam onto the sample;
one or more processors; and
a memory storing instructions that when executed on the one or more processors causes the charged particle microscope system to:
generate a 3D fiducial in the sample by generating a 3D void in the sample according to the 3D fiducial configuration, the 3D fiducial having a depth greater than or equal to a depth of the sample, and cross sections of a 3D fiducial generated using the 3D fiducial configuration having a same shape in parallel cross sections;
remove a first portion of the sample to expose a first surface, the first surface including the 3D fiducial;
generate a first image within a consistent reference frame determined by the 3D fiducial configuration by imaging at least a portion of the first surface, wherein the portion of the first surface includes the 3D fiducial and a first cross section of a structure in the sample;
remove a second portion of the sample to expose a second surface after imaging the portion of the first surface, the second surface including the 3D fiducial;
generate a second image within the consistent reference frame by imaging at least a portion of the second surface, wherein the portion of the second surface includes the 3D fiducial and a second cross section of the structure;
determine, based on the first image, a first relative position between the 3D fiducial in the first image and the first cross section of the structure;
determine, based on the second image, a second relative position between the 3D fiducial in the second image and the second cross section of the structure; and
determine, based on the first relative position and the second relative position, a positional relationship between the first cross section of the structure and the second cross section of the structure,
wherein, within the consistent reference frame, representative positional values of the 3D fiducial included in the second surface are consistent with representative positional values of the 3D fiducial included in the first surface.
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