In my talk, I will give an overview about imaging and local milling of two-dimensional nanostructures with helium ion microscopy (HIM). In particular, carbon nanomembranes (CNMs), graphene and biological cell membranes will be discussed. CNMs are made by a combination of molecular self-assembly, radiation-induced cross-linking and the detachment of the cross-linked monolayer from its substrate. Although free-standing CNMs cannot be imaged by light microscopy, charged particle techniques can visualize them. However, CNMs are electrically insulating, which makes them sensitive to charging. The same is true for biological cell membranes. I will demonstrate that HIM is particularly well suited for imaging such insulating membranes due to its efficient charge compensation tool. In particular, I will discuss the effects of sample charging, imaging of multilayers and imaging artefacts for CNMs as a model system. Furthermore, I will show that the focused helium ion beam of the HIM can be utilized to create nanopores with diameters down to 1.3 nm in insulating as well as conducting membranes. An analysis of the nanopore growth behaviour allows determination of the profile of the helium ion beam.