Transmission electron microscopy (TEM) imaging is one of the few techniques available for direct observation of the microstructure of ultrafiltration cakes. TEM images yield local microstructural information in the form of two-dimensional grayscale images of slices a few particle diameters in thickness. This work presents an innovative particle-by-particle reconstruction scheme for simulating ultrafiltration cake microstructure in three dimensions from TEM images. The scheme uses binarized TEM images, thereby permitting use of lesser-quality images. It is able to account for short- and long-range order within ultrafiltration cake structure by matching the morphology of simulated and measured microstructures at a number of resolutions and scales identifiable within the observed microstructure. In the end, simulated microstructures are intended for improving our understanding of the relationships between cake morphology, ultrafiltration performance, and operating conditions.