We. present fabrication schemes for nanoscale molecular junctions, which allow the deposition of molecules after the fabrication steps that can uncontrollably affect the electrical properties of the molecular layers. The two techniques described here use shadow mask evaporation and nanotransfer printing. In order to make reliable contacts with the molecules (or molecular monolayers) the morphology of the contacting metals has to be optimized and controlled. We therefore characterize the surfaces of the contacting metals using scanning electron microscopy and scanning probe microscopy at various stages of the fabrication. Based on these results we developed methods, to improve the morphology in order to realize more reliable metal-molecule contacts. It is shown that improvement of the surface topography of the metals indeed leads to metal-molecule-metal junctions with a very low failure rate. (c) 2005 American Vacuum Society.