The use of magnetic nanoparticles in the development of ultra-high-density recording media is the subject of intense research. Much of the attention of this research is devoted to the stability of magnetic moments, often neglecting the influence of dipolar interactions. Here, we explore the magnetic microstructure of different assemblies of monodisperse cobalt single-domain nanoparticles by magnetic force microscopy and magnetometric measurements. We observe that when the density of particles per unit area is higher than a determined threshold, the two-dimensional self-assemblies behave as a continuous ferromagnetic thin film. Correlated areas (similar to domains) of parallel magnetization roughly ten particles in diameter appear. As this magnetic percolation is mediated by dipolar interactions, the magnetic microstructure, its distribution and stability, is strongly dependent on the topological distribution of the dipoles. Thus, the magnetic structures of three-dimensional assemblies are magnetically soft, and an evolution of the magnetic microstructure is observed with consecutive scans of the microscope tip.