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A key issue to push molecular devices toward a new range of applications is the ability to master large scale integration while preserving the device's functionality. Furthermore, providing extra tunability of the device by external parameters, such as gating in a transistor-like configuration, is highly suited for molecular electronics. Large area molecular junctions in crossbar geometry have demonstrated high yields and compatible and compatible fabrication with Complementary Metal Oxide Semiconductor (CMOS) technology. However, such a device's geometry favors diffusion of metallic atoms in the molecular layer and gives a very limited access to perform electrical or optical gating on molecules. In this work, we propose a new molecular junction architecture going behind these limits. We report a robust approach for the fabrication of molecular junctions based on the electrografting of a nanometer-thick molecular layer in high aspect ratio metallic nanotrenches. Nanotrenches are obtained by edge-mediated shadow deposition, resulting in laterally aligned electrodes with a 10.3 nm ± 3.3 nm average spacing along a 20 μm length. An in-solution electroreduction of diazonium salts is subsequently performed to fill the nanotrenches by a thin oligomeric layer of anthraquinone molecules. Electronic transport measurements performed at room temperature reveal the ability to produce stable molecular devices. Such a new junction's engineering offers the key advantages of high fabrication yield, great amenability for compact assembly, and reduced leakage current. The proposed architecture opens interesting perspectives to investigate fundamental and applied questions in molecular electronics, in which coupling of the molecules with external stimuli is required. [ABSTRACT FROM AUTHOR]