In this thesis I describe the design and characteristics of a variety of superconducting devices fabricated using focused Helium ion beam. Early chapters are dedicated to summarizing the mechanics of superconductors and discussing the theoretical operating principles underlying Josephson junctions and superconducting quantum interference devices (SQUIDs). In this thesis the superconducting devices are made using $Y Ba_2 Cu_3 O_{7 - \delta}$ (YBCO) and Niobium films.

Using a Helium ion microscope, I am able to modify the electronic structure of the superconducting material by directly writing induced disordered regions that define the structure and geometry of the devices. By carefully choosing the dose of ion irradiation I can accurately set the operating characteristic, critical current and normal state resistance, of the Josephson junctions as well as creating highly insulating regions allowing me to define device geometries at the nanometer scale.

Experiments using YBCO films outline the types of Josephson junctions I can make with this fabrication technique. YBCO Junctions are characterized over a wide range of temperature. I characterize the critical current response in the presence of a magnetic field and demonstrate the AC Josephson effect through the emergence of Shapiro steps in the IV curve. Much of my work on YBCO is dedicated to the design and characterization of highly sensitive SQUID magnetometers. I successfully integrated the SQUID magnetometer on a commercial pulsed tube cooler equipped with a peizo-controlled stage probe head for magnetic materials analysis. This system has an operating temperature range between 1-50K. A similar lower noise iteration of this design was found to have a field noise of $540 fT / \sqrt{Hz}$ and a flux noise of $2 \mu \Phi_0 / \sqrt{Hz} $ at 1Khz making it the lowest noise YBCO SQUID smaller than $500\mu m$ ever made.

I fabricated and characterized the first Josephson junctions on niobium films made with focused Helium ion beam. This technique can mill the Niobium with resolution as small as 40nm. Junction fabrication is analyzed at a wide range of doses, and I found Josephson effects in devices radiated from 50,000 to 15,000,000 ions/nm. Junctions were characterized at a wide range of temperatures showing the onset of hysteresis to the IV curve as temperature decreases. I also performed characterizations of the junctions in magnetic field and showed the formation of Shapiro steps to the IV curve when junctions are in the presence of microwave radiation. I fabricated arrays of Josephson junctions on niobium film and analyzed the optimal spacing for junctions in the arrays. I demonstrated the operation of arrays with up to 100 junctions in series and showed giant flat Shapiro steps at voltages of up to 1.32mV. I showed how these junction arrays can be scaled up and integrated in Josephson arbitrary waveform synthesizer or DC voltage standard devices. Lastly, I fabricated and characterized the first niobium SQUID made with focused helium ion beam induced disorder junctions.