The growing field of molecular spintronics is an auspicious route to future concepts of data storage and processing. It has been reported that the hybridization of the electronic structures of non-magnetic organic molecules and ferromagnetic transition-metal (FM) surfaces can form new magnetic units, so-called hybrid molecular magnets, with distinct magnetic properties, which promise molecular spintronic devices with extremely high information density and low energy consumption. The investigation and profound understanding of these device concepts require the formation of clean and epitaxial interfaces between the surface of a FM bottom electrode and molecular thin films. This can only be realized under ultra-high vacuum conditions. In addition, the FM electrodes must be grown on an insulating substrate to electrically separate neighboring devices. Here, we report on procedures to realize an entirely in-situ preparation of mesoscopic test devices featuring structurally and chemically well-defined interfaces. Au(111)-buffered Co(0001) electrodes are deposited by molecular-beam epitaxy onto sapphire or mica substrates using a shadow-mask to define the geometry. The surface quality is subsequently characterized by scanning tunneling microscopy (STM) and other surface science analysis tools. 2,7-dibenzyl 1,4,5,8-naphthalenetetracarboxylic diimide (BNTCDI), which serves as an exemplary molecule, is sublimed through another shadowmask, and the interface formation in the monolayer regime is also studied by STM. Finally, we deposit a Cu top electrode through yet another shadow-mask to complete a mesoscopic (200 x 200 mu m(2)) test device, which reveals in ex-situ transport measurements for the Co/BNTCDI/Cu junction non-metallic behavior and a resistance-area product of 24 M Omega.mu m(2) at 10 K.