Three-dimensional mapping of microscopic surface structures is important in many applications of technology and research, including areas as diverse as microfluidics, MEMS and geoscience. How- ever on the nanoscale, using established techniques for such imaging can be extremely challenging. Scanning helium microscopy (SHeM) is a new technique that uses neutral helium atoms as a probe, enabling completely non-destructive imaging. The technique is broadly applicable and ideal for many otherwise difficult to image materials such as insulators, ultra-thin nano-coatings and biological sam- ples. Here we present a method for implementation and operation of a stereo helium microscope, by applying the photometric stereo method of surface reconstruction to helium microscopy. Four detectors around the sample are typically required, but we show how sample rotation can be used to perform stereo reconstruction with a single detector instrument, or to improve the quality of the reconstructed surface by increasing the number of independent measurements. We examine the quality of the reconstructed surface and show that for low aspect ratio good absolute height is recovered. For features with height/width ∼ 1 the shape of the surface is still recovered well (8% error) despite multiple scattering and masking of the helium beam by surface topography. Therefore it is possible to perform accurate reconstruction of the shape of nanoscale structures with a height to width ratio of at least unity.