We demonstrate that spatial confinement can be used to control the orientational and translational order of cubic nanoparticles. For this purpose we have combined X-ray scattering and scanning electron microscopy to study the ordering of iron oxide nanocubes that have self-assembled from toluene-based dispersions in nanofluidic channels. An analysis of scattering vector components with directions parallel and perpendicular to the slit walls shows that the confining walls induce a preferential parallel alignment of the nanocube (100) faces. Moreover, slit wall separations that are commensurate with an integer multiple of the edge length of the oleic acid-capped nanocubes result in a more pronounced translational order of the self-assembled arrays compared to incommensurate confinement. These results show that the confined assembly of anisotropic nanocrystals is a promising route to nanoscale devices with tunable anisotropic properties.