High resolution STEM of microelectronic and related materials requires samples that are free of artifacts on both the nano and atomic scales. Traditional preparation methods are supplemented by cryogenic ion milling and argon-oxygen plasma cleaning. A variety of side-entry sample holders are available to support subsequent imaging and analysis. These holders include those designed for 3D tomography, holography, electrical biasing of n-p junctions, nanopositioning of probes with respect to the sample surface, and induction of magnetic fields in the plane of the specimen. Imaging in dark field using a high angle, annular detector can support an analysis specific to a particular column of atoms within an engineered material.