The primary objectives of failure analysis on structurally complex semiconductor devices are often to determine a defect's location and composition. Determining exactly how these defects propagate through a sample in three dimensions, to confirm a failure mode, is often elusive. This paper discusses characterizations of two defect types to illustrate a technique of sequentially imaging whisker type defects from orthogonal orientations using TEM/STEM. The first type is a high resistance short between two metal lines that is best imaged using STEM in order to observe subtle differences in material composition. The second is a crystalline dislocation through an optoelectronic device that is best observed using TEM. Details of resistive short characterization and crystalline defect characterization performed are provided. TEM/STEM has shown to be a practical tool for locating defects prior to cross sectional analysis. This allows defects to be located and characterized in three dimensions.