Mechanical oscillators became a main focus of research in recent years for potential applications in biomolecule detectors. We recently demonstrated the feasibility of a scheme based on twin cantilevers with a sensitivity down to the single molecule. This approach is extremely promising under the condition that the two terminals of the device can be functionalized with high selectivity and nanometric accuracy by linker molecules. Here we demonstrate a chemo-mechanical method to achieve the intrinsically aligned functionalization of two silicon surfaces, which can be separated by a gap controllable with nanometric precision. The chemical binding of the target molecules in the selected position is obtained through a cycloaddition reaction which exploits the reactivity of the freshly cleaved surfaces that form when the cantilever gap is created. The general validity of this approach is shown by the use in different chemical environments of two compounds with different reactive functional groups.