Continued pursuit of better superconducting devices and an understanding of how the focused ion beam evolves in a complex material are the primary motivations behind this work. The materials of interest are MgB2 and Co-doped Ba122. Superconducting properties of MgB2 were discovered in 2001. It is the first superconductor recognized as a multigap superconductor. Owing to its high Tc of ~39K, electronic circuits based on this material are expected to operate at a much higher temperature (~25 K) than low-temperature superconductors, using compact cryocoolers. Co-doped Ba122 is also a multigap superconductor which belongs to Fe-based superconductor (FeSC) family. The undoped Ba122 compound is a metal exhibiting antiferromagnetism which coexists with superconducting phase up to a certain doping level. The optimally electron-doped BaFe2As2 exhibits the transition temperature Tc of ~21 K which corresponds to the top of the “dome” in the phase diagram. While the Fe-based SC may not signify a particular advance in terms of practical applications, many unique aspects make them worth studying. In particular, the superconducting gap symmetry and structures which appear to be quite different from family to family and not yet fully understood. We report on investigating the normal-state, and superconducting properties of Co-doped BaFe2As2 and MgB2 thin films irradiated at room temperature using a 30-keV focused He+ ion beam in helium ion microscope (HIM). R-T measurement was carried out to extract the dose dependence for Tc and resistivity p0 of the irradiated region. We observed an increase in p0 and a decrease in Tc down to complete suppression of superconductivity for both materials, although the trend of the changes was quite different. In addition, for Ba122, the data for ΔTc ⁄ Tc0 versus measured change in resistivity favors s± over s++ symmetry. Using TRIM software, the projected range and the damage density distribution of the He+ ions were tracked in the samples. Single track irradiation sites for MgB2 sample were characterized using FIB extraction/TEM. The TEM micrographs reveal the subsurface damage density contours that evolve with increasing dose. The Josephson effect is a unique phenomenon that gives direct access to the phase difference �� of the macroscopic wave functions that describe the superconducting state. Josephson junction is also appealing for engineering application in superconducting electronics. Having found the dose at which complete suppression of Tc occurs from the first part of the study, a fabrication process was developed to produce planar Josephson junctions from MgB2 and Co-doped Ba122. The Josephson coupling across the barrier for both materials was observed. MgB2 Josephson junctions showed resistivity shunted junction (RSJ) I-V curve with excellent uniformity and reproducibility. We have also demonstrated tens of planar MgB2 Josephson junctions operating coherently in series arrays. 60 Josephson junction series arrays successfully developed with less than 4% spread in critical current at 12 K. Under microwave radiation, flat giant Shapiro steps up to 150 μA width appear at voltages Vn=NnΦ0f, where N is the number of junction in the array, �� is an integer representing Shapiro step index, and f is the applied microwave frequency. The uniformity and close spacing of JJs in the arrays are significantly better than MgB2 multi-junction devices made by other techniques. It has been a huge success in showing the feasibility of this technology for pursuing superconducting digital electronics, Josephson voltage standards and arbitrary function generators in particular, in MgB2 with ≥ 20K operating temperature. / Physics