SummaryThree-dimensional focused ion beam (FIB) tomography is increasingly being used for 3D characterization of microstructures in the 50 nm-20 μm range. FIB tomography is a destructive, invasive process, and microstructural changes may potentially occur during the analysis process. Here residual stress and crack morphologies in single-crystal sapphire samples have been concurrently analyzed using Cr 3+ fluorescence spectroscopy and FIB tomography. Specifically, maps of surface residual stress have been obtained from optically polished single-crystal alumina [surface orientation (1ī 0 2)], from FIB milled surface trenches, from Vickers micro-indentation sites (loads 50 g-300 g), and from Vickers micro-indentation sites during FIB serial sectioning. The residual stress maps clearly show that FIB sputtering generates residual stress changes. For the case of the Vickers microindentations, FIB sputtering causes significant changes in residual stress during the FIB tomographic serial sectioning. 3D reconstruction of the crack distribution around microindentation sites shows that the cracks observed are influenced by the location of the FIB milled surface trenches due to localized stress changes.