The fabrication of silicon nitride membrane substrates and their use in studies of polymer thin films are described. As an integral part of a wafer, these membranes are both self-supporting and transparent for transmission electron microscopy (TEM). Therefore, the same polymer film can be spin-cast on the substrate and, without being removed, studied by a variety of techniques, including TEM, and atomic force microscopy (AFM). To demonstrate the utility of these substrates in characterizing both global and local film morphology, experimental results are presented on polystyrene-polymethylmethacrylate diblock copolymers in the ultrathin him limit, using optical microscopy together with combinations of AFM and TEM at the same location. The addition of microfabricated structures to these substrates, such as planar electrodes is also discussed.