A method of modifying a resonant frequency of a quantum device includes generating an ion beam having a beam energy and exposing a surface of the quantum device to the ion beam for an exposure time. The ion beam is incident onto the quantum device at an oblique angle that is less than 90 degrees as measured from the surface of the quantum device. The quantum device includes a Josephson junction, the ion beam exposing the quantum device proximate to the Josephson junction to modify a property of the Josephson junction, the property being associated with the resonant frequency of the quantum device.