Since its first application to the field more than 10 years ago, micro-computed tomography (micro-CT) has been a state-of-the-art technology in the study of insect morphology and anatomy. Despite showing great potential for various types of non-destructive ‘dissections’, the method has, however, seen very limited use in descriptive taxonomy. Here we describe a method for carrying out virtual dissections of the genitalia in male Lepidoptera based on case studies involving the butterfly Argynnis paphia and the hawkmoth Cephonodes hylas. We demonstrate how a standard micro-CT scanner in conjunction with freely available software can distinguish and illustrate taxonomically important characters, and propose a workflow by which valuable material (such as Linnaean types) can be made available as digital loans, and how users can subsequently carry out ‘virtual dissections’. We emphasize that micro-CT scanning does not remove the need for real dissections and morphological expertise to confidently evaluate virtual ‘dissections’.