Currently, the helium ion microscope (HIM) can be operated in three imaging modes; ion induced secondary electron (SE) mode, Rutherford backscatter imaging (RBI) mode, and scanning transmission ion imaging (STIM) mode. This paper will provide an overview of microscope’s ion source, its ion optics, the system architecture, the fundamentals of these three imaging modes and many FA related examples. Recently integrated with the microscope are a Rutherford Backscatter (RBS) detector for materials analysis and a gas injection system (GIS) for material modification. We will describe this new hardware and suggest how these additions could also contribute to the helium ion microscope being an important failure analysis tool.