Focused-Ion Beam Scanning Electron Microscopy (FIB-SEM) tomography is a high resolution three-dimensional (3D) imaging method with applications in failure analysis and metrology of semiconductor devices. For the smallest logic and memory structures currently in use, it requires single-digit nanometer 3D resolution. In this resolution range, avoiding distortion artifacts in the data becomes crucial. We present examples and discuss ways to reduce the likelihood of such artifacts during the data acquisition, as well as how to mitigate them in post-processing, and therefore increase the data quality.