Miscible (Al/Nb) and immiscible (Cu/Nb) nanometallic multilayer systems were characterized by means of transmission electron microscopy techniques, primarily by automated crystallographic orientation mapping, which allows for the resolution of crystal structures and orientations at the nanoscale. By using this technique, distinctive Nb orientations in relation to the crystallographic state of the Al and Cu layer structures can be observed. Specifically, the Al and Cu layers were found to consist of amorphous, semi-amorphous, and crystalline regions, which affect the overall multilayer microstructure.