This thesis describes the development and applications of sub-micron current-perpendicular-toplane devices fabricated by three-dimensional etching with a focused ion beam microscope. This technique was applied to a range of materials, including the study of c-axis Josephson junctions in the high temperature superconductor Tl2Ba2CaCu2O8, the fabrication of superconducting quantum interference devices with sub-micron loop areas, and GaN light emitting diodes. The main body of research was carried out in the study of Nb based Josephson junctions working at a temperature of 4.2 K. Junctions with normal metal, insulating and ferromagnetic barriers were characterised, as well as the first metallic antiferromagnetic Josephson junctions using γ-Fe50Mn50 as the barrier. ‘Pseudo-spin-valve’ Josephson junctions were also created using a Co/Cu/Fe20Ni80 barrier. In this case the relative orientation of the magnetic moments of the Co and Fe20Ni80 could be changed with an applied magnetic field. The magnetoresistance and critical current of the device showed a strong correlation, implying a direct influence of the magnetic structure of the device on the critical current.