Recent advances in quantum technologies are highly influencing the current technological scenario. Hybrid devices combining superconductors and topological insulators represent an excellent opportunity to study the topological superconducting phase, which offers interesting features that might have significant implications in the development of quantum sensing and quantum computing. Furthermore, focused ion beam techniques, whose versatility enables to create sophisticated devices with high degree of customization, can enhance the creation of complex devices. Here, we develop a novel approach for creating single-crystal devices that is applied to the fabrication of superconducting devices based on topological insulator Bi2Se3 in a geometry characteristic of a superconducting quantum interference device. Characterization of these devices reveals that superconductivity is induced in our crystal and the supercurrent is modulated by applying an external magnetic field. These results open the way to tailoring the response of hybrid devices that combine superconductors and topological insulators by focused ion beam techniques.