The methods of superconducting device fabrication by lithography and multilevel pprocessing usually require a number of processing steps with lithographic resolution and alignment adequate for the scale of the device be fabricated. As an alternative, the focused ion beam (FIB) microscope is increasingly being used to actively fabricate devices. A major advantage of using a FIB compared to other beam lithography methods is its flexibility. It allows in-situ, high resolution milling (~8 nm at a beam current of 1 pA) to a variety of depths, and imaging (6 nm) of the sample. In this paper we describe our development of junction fabrication techniques using the FIB and their application in creating a range of potential sensor devices. The paper will cover both nanoscale SQUID devices and other structures with potential quantum electronics applications.