We report the formation of solid-state nanopores using the highly focused ion beam and lithographic capabilities of a scanning Helium Ion Microscope (HIM). We will discuss several aspects of the fabrication process, offering the advantage of high sample throughput along with fine control over nanopore dimensions. We will compare characteristics of the resultant devices with those made by the established technique of transmission electron microscope milling and demonstrate the utility of our nanopores for biomolecular analysis.