Method and system for imaging three-dimensional feature

A method for imaging a sample, comprising:

• locating a first fiducial on a first sample surface at a first sample depth;
• milling the sample from the first sample depth to a second sample depth to expose multiple first sample surfaces, and acquiring multiple first sample images including the first fiducial and a region of interest (ROI) on the exposed multiple first sample surfaces using a charged particle beam at a first focal depth, wherein each of the multiple first sample images corresponds to one of the multiple first sample surfaces from the first sample depth to the second sample depth;
• locating a second fiducial, wherein the second fiducial is formed during or after removing the portion of the first sample surface;
• milling the sample from the second sample depth to a third sample depth to expose multiple second sample surfaces including the ROI, and acquiring multiple second sample images including the second fiducial and the ROI on the exposed multiple second sample surfaces using the charged particle beam at a second, different, focal depth, wherein each of the multiple second sample images corresponds to one of the multiple second sample surfaces from the second sample depth to the third sample depth;
• and
• reconstructing a feature in the ROI by aligning the multiple first sample images and the multiple second sample images based on locations of the first fiducial in the multiple first images, locations of the second fiducial in the multiple second images, and a location of the first fiducial relative to the second fiducial in a sample plane perpendicular to a depth direction.

A charged particle microscopy system, comprising:

• a sample holder for positioning a sample;
• an ion beam source for directing an ion beam towards the sample held by the sample holder;
• an electron beam source for directing an electron beam towards the sample;
• and
• a controller includes a non-transitory memory for storing computer-readable instructions that when executed, causing the controller to:
• locate a first fiducial on a first sample surface at a first sample depth;
• remove at least a portion of the first sample surface to expose a second sample surface;
• locate a second fiducial, wherein the second fiducial is formed during or after removing the portion of the first sample surface;
• remove at least a portion of the second sample surface to expose a third sample surface including a region of interest (ROI) at a third sample depth;
• acquire a first sample image including the second fiducial and the ROI at the third sample depth;
• and
• determine a location of the ROI at the third sample depth relative to the first fiducial in a sample plane perpendicular to a depth direction based on a first location of the first fiducial relative to the second fiducial in the sample plane and a second location of the ROI relative to the second fiducial in the sample plane, wherein the second location is determined in the first sample image.