A micro-optoelectromechanical system based device with aligned structures comprises at least one optical structure formed in a silicon layer of the device and at least one optical fiber connection structure that is self-aligned with the at least one optical structure. In embodiments, the at least one optical fiber connection structure is formed in a substrate of the device and may comprise a V-groove. In other embodiments, the at least one optical structure may comprise a waveguide. A nitride layer may be formed on at least a portion of the waveguide. In various embodiments, the silicon layer may be a single-crystal-silicon layer of a silicon-on-insulator wafer. A method for fabricating a micro-optoelectromechanical system based device with aligned structures is provided in which the at least one optical structure and the at least one optical fiber connection structure are defined using the same masking layer.