This paper demonstrates that transmissive or partially transmissive scenes imaged by digital in-line holographic microscopy (DIHM) can be reconstructed as a threedimensional (3-D) model of the imaged volume from a single capture. This process entails numerical reconstruction, segmentation and polygonisation. Numerical reconstruction of a digital hologram captured using a DIHM set up is performed at equally spaced depths within a range. In the case of intensity modulating objects, segmentation of each of the reconstructed intensity images produces a contour slice of the scene by applying an adaptive threshold and border following. These slices are visualised in 3-D by polygonising the data using the marching cubes algorithm. We present experimental results for a real world DIHM capture of a partially transmissive scene that demonstrates the steps in this process.