3D reconstruction of biological material, such as cells, enzymes, and molecules, represents a significant challenge to scientists today. Not only are biological samples particularly hard to image as they are prone to charge build up and easily damaged, but for useful reconstructions images with a huge field of view (on the order of microns) and nanometre resolution are required. This technology would greatly improve our understanding biological processes including cell signalling, gene expression, protein folding in addition to having applications within nanoelectronics, photonics, nanocomposites, and nanoporous material. This experiment looked at a novel approach for 3D imaging by using the Helium-Ion Mircoscope (HIM). It was demonstrated that the HIM has several advantages over more commonly used scanning electron microscopes (SEMs) such as a smaller probe size (and thus higher resolution) and better charge compensation that allowed for the imaging of uncoated biological samples. In addition a qualitative 3D stereo-image was created from SEM images of a coated cancer cell and a process of calculating quantitative measurements of feature dimensions from stereo-pairs was created. Future work will develop a method for 3D modelling biological samples and compare 3D reconstruction from the HIM with the ones created from SEM images.