Provided are methods to improve tomography by creating fiducial holes using charged particle beams, and using the fiducial holes to improve the sample positioning, acquisition, alignment, reconstruction, and visualization of tomography data sets. Some versions create fiducial holes with an ion beam during the process of milling the sample. Other versions create in situ fiducial holes within the TEM using the electron beam prior to acquiring a tomography data series. In some versions multiple sets of fiducial holes are made, positioned strategically around a region of interest. The fiducial holes may be employed to properly position the features of interest during the acquisition, and later to help better align the tilt-series, and improve the accuracy and resolution of the final reconstruction. The operator or software may identify the holes to be tracked with tomography feature tracking techniques.