Museum collections are currently undergoing extensive digitisation in the form of three dimensional (3D) imaging of specimens, and palaeontological holdings are no exception. Improved data accessibility brings benefits not only to scientists but also to the general public and science promotion. Microfossils, however, remain a distinct entity in this process because their small size, more complex sample preparation, and higher equipment requirements bring additional challenges. Two representative groups, chitinozoans and scolecodonts, whose average size ranges from 100 to 1000 μm, were chosen to test suitable methods for 3D modelling and imaging of their inner structures. Earlier 3D imaging techniques were predominantly destructive, rendering them unsuitable for type material and other unique specimens. Our main objective was to introduce and test two 3D modelling approaches appropriate for the online presentation of museum collections, and to develop a repeatable sample preparation protocol for future studies. X-ray computed tomography (CT), specifically micro-CT and submicron-CT (CT with achievable resolution in the micrometre and sub-micrometre range, respectively), and microphotogrammetry based on scanning electron microscopy (SEM) images were applied. In addition, the acquired 3D models can be used for science outreach and educational purposes, including the production of 3D-printed models.