Precise spatial organization and electronic coupling between quantum dots are pivotal for many potential applications. Typical spherical quantum dots in assemblies are separated by organic ligands and hence weakly coupled. GaSe nanoparticles are disk-like particles that are four atoms thick with tunable lateral dimensions. Previous spectroscopic investigations indicate the formation of nanoscale aggregates in which the quantum dots are strongly coupled. In this report, we show that the anisotropic properties of these particles may be exploited to assemble surface-stabilized superstructures with well-defined distances between the quantum dots. By changing the ligands adsorbed on the nanoparticle edges, three distinct aggregate morphologies can be produced. The surface chemistry of GaSe orients the nanoparticles on a gold surface and induces stacking in the surface normal direction. The discrete heights of such stacked aggregates suggest that the layers are held together by van der Waals interactions with a regular spacing. Such structures, with their well-defined electronic coupling, have potential implications in fundamental studies of photoinduced charge transfer and transport, as well as device fabrications.