In this work we present a characterization of the bidisperse ferrofluid microstructures that appear in thin layers of ferrofluid. These layers have been studied by a combination of Langevin dynamics simulations and density functional theory. Our results allow us to compare the microstructures that exist in quasi-two-dimensional ferrofluid nanolayers with the microstructures found in three-dimensional bidisperse ferrofluids. Furthermore, our results allow us to explain the influence of the geometry of the sample on the topology and size-distribution of the observed aggregates of magnetic nanoparticles.