The formation of organized structures of magnetic nanoparticles have been studied by scanning probe microscopy when depositing Ni nanoclusters on conducting (gold on HOPG) substrates. In this case magnetic Ni nanoparticles formed by laser electrodispersion technique based on laser ablation (size of particles ∼ 2.5 nm) form highly ordered superstructures, including helical (double helix with outer diameter ∼ 10 nm, distance between sequences ∼ 5 nm, length of such helix is typically hundreds of nm), linear (chains of clusters), etc. The structures discovered were investigated also by STS methods, with clear demonstration of Coulomb blockade effect over single nanoclusters. The results of calculations for dipole-dipole and exchange interaction of magnetic nanoparticles support such formation of helix-like structures.