A simple fabrication scheme for molecular electronic junctions is presented with multi-walled carbon nanotubes (MWCNTs) as the top electrodes. Results indicate that our approach retains the molecular character of the chosen molecules [a self-assembled mono-layer of octadecanethiol on gold bottom electrodes] and opens the door for studying a wide variety of organothiol candidates for molecular electronics. The fabrication scheme is designed in a way that it can be modified into all-carbon devices in the future by using graphitic carbon bottom electrodes functionalized with nitrozoabenzene, for example, and MWCNTs or graphene as the top electrodes. Alternatively, the scheme is applicable for all-gold devices with gold bottom electrodes and gold nanowire top electrodes.