In this paper we studied three major issues that have challenged focused ion beam (FIB) circuit edit practices: via overetching, via composition which affects via resistance, and uniformity of via fill. These issues may become critical as minimal circuit dimensions reduce in the future. We investigated the amorphization induced by FIB gas assisted etch and ion beam induced metal deposition in high aspect ratio vias, using bright and dark field transmission electron microscopy images. A simple intuitive model is introduced to explain the differences in amorphization layer thicknesses between the steep FIB via sidewalls and the via floor. We analyze the dependence of FIB via purity on depth using EDS. Directions for future FIB applications are discussed in the paper along with a FIB via fill strategy.