Surfaces with artificial roughness were generated by deposition of nanoparticles on single crystalline substrates. Nanoparticles with an average size ≈ 15 nm were produced by inert gas condensation and deposited in situ on the substrate mounted inside a modified ultra high vacuum (UHV) transmission electron microscope (TEM). We have investigated the smoothing behavior on annealing based on the difference in surface energies between cluster and substrate and their heat of mixing. The cluster substrate combination Co/Cu(100) was chosen as a model system in which the cluster has a significantly higher surface energy than the substrate. Upon deposition at 600 K, the clusters do not remain on the surface, but rather burrow into the substrate. This is confirmed by a detailed strain analysis of the particles. Nanoparticles in the system Ge/Si(100) in contrast have a lower surface energy than the substrate and are completely miscible. The particles assume the substrate orientation around 700 K. At 900 K coherent islands form which are arranged in clusters of 4 in the form of a square. The reason for this previously unobserved pattern is not yet understood.