We report a method for fabricating nanogaps directly with electron beam lithography (EBL). The primary resolution-limit of EBL, electron back-scattering, is reduced dramatically by using a thin-film as a substrate. We show that this resolution enhancement allows one to fabricate metal electrodes with separation from arbitrarily large to under one nanometer. Furthermore, because these nanogaps are on a thin film, they can be imaged with high-resolution transmission electron microscopy (HRTEM). Using these nanogaps we measured the charge transport through several coupled PbSe nanocrystals and correlated the data with detailed structural information obtained by performing HRTEM on the same device.