Molecules with versatile functionalities and well-defined structures, can serve as building blocks for extreme nanoscale devices. This requires their precise integration into functional heterojunctions, most commonly in the form of metal-molecule-metal architectures. Structural damage and nonuniformities caused by current fabrication techniques, however, limit their effective incorporation. Here, we present a hybrid fabrication approach enabling uniform molecular gaps. Template-stripped lithographically-patterned gold electrodes with sub-nanometer roughness are used as the bottom contacts upon which the molecular layer is formed through self-assembly. The top contacts are assembled using dielectrophoretic trapping of colloidal gold nanorods, resulting in uniform sub-5 nm junctions. In these electrically-active designs, we further explore the possibility of mechanical tunability. The presence of molecules may help control sub-nanometer mechanical modulation which is conventionally difficult to achieve due to instabilities caused by surface adhesive forces. Our approach is versatile, providing a platform to develop and study active molecular gaps towards functional nanodevices.