Insects have evolved numerous adaptations to survive a variety of environmental conditions. Given that the primary interface between insects and the environment is mediated through their skin or cuticle, many of these adaptations are found in extraordinary cuticle diversity both in morphology and structure. Not all of these adaptions manifest themselves in changes in the chemical composition of the cuticle but rather as elaborations of the surface structures of the cuticle. Typically the examination of these micro- and nanoscale structures has been performed using scanning electron microscopy (SEM). Typically, in order to decrease surface charging and increase resolution, an obscuring conductive layer is applied to the sample surface, but this layer limits the ability to identify nanoscale surface structures. In this paper we use a new technology, helium ion microscopy (HIM) to examine surface structures on the cuticle of wild type and mutant Drosophila. Helium ion microscopy permits high resolution imaging of biological samples without the need for coating. We compare HIM to traditional SEM and demonstrate certain advantages of this type of microscopy, with our focus being high resolution characterization of nanostructures on the cuticle of Drosophila melanogaster and potentially other biological specimens.