The development of combined focused ion beam and scanning electron microscopes has enabled significant advances in the characterization of the 3-D structure of materials. The repeated removal of thin layers or slices with an ion beam and imaging or mapping the chemical or crystallographic structure of each slice enables a 3-D reconstruction from the images or maps. The accuracy of the reconstruction thus depends on the accuracy with which the slice thickness is measured and maintained throughout the process, and the alignment accuracy of the slices achieved during acquisition or by postacquisition corrections. A survey of papers published in this field suggests that the reconstruction accuracy is not often considered or reported. Using examples from examination of the 3-D structure of hardmetals, issues affecting the accuracy of slice thicknesses and image realignments are examined and illustrated and potential errors quantified by the use of fiducial markers and the expected isotropy of the hardmetal structure itself.