In this chapter, we discuss controllable HIM modication and sub-nanometer metrology, with graphene used as an example. Challenges in graphene characterization and modication will be rst introduced in the following section. To understand the HIM’s potential to address these challenges, the basic principles of the tool will be explained. e next two sections will be focused on the applications of HIM in high-quality imaging and ultrane modication. Our discussion will not be limited within the graphene research. To broaden the scope, we will introduce applications of the HIM in other relevant elds wherever appropriate.