1. A method of tomographic analysis of a pillar-shaped sample, comprising: (a) directing one or more charged particle beam at a sample to shape the sample into a pillar shape for tomography; (b) positioning the sample in a first position and directing one of the charged particle beams in a dwell operating mode at the sample to create a first fiducial hole in the sample; (c) after creating the first fiducial hole, positioning the sample for a series of tomographic data scans; (d) conducting a series of tomographic data scans of the sample; and (e) based on the position of first fiducial hole in the tomographic data scans, improving the accuracy of tomographic data in the tomographic data scans.