We investigated the dewetting, surface roughness, and ordering of cylindrical nanodomains in polystyrene-block-poly(methyl methacrylate), P(S-b-MMA), ultrathin films of approximately monolayer thickness on bare silicon substrates (SiOx/Si) and substrates coated with end-grafting PMMA (PMMA-SiOx/Si) and PS (PS-SiOx/Si) homopolymers. For films with asymmetric wetting boundaries on SiOx/Si and PMMA-SiO x/Si, annealing caused relief structures (holes and islands) locating on top of an underlying P(S-b-MMA) wetting monolayer. The interfaces of the destabilized thin films on polar substrates have a smooth free surface. In addition, a surface undulation in film thickness to achieve the commensurability of film thickness with the nanodomain spacing facilitates the ordering of internal nanostructures. In contrast, for symmetric wetting boundaries on PS-SiOx/Si, thin films that resisted dewetting on a PS brush have a rough free surface. In the absence of undulations in thickness, a perturbation, as result of chain stretching, in the interdomain spacing yielded small in-plane randomly oriented monograins on PS-SiOx/Si. Consequently, the free surface roughening was allowable to occur due to preferential segregation of excluded polymer chains from monograin boundaries onto the free surface. Finally, we demonstrate that the roughnesses between the interfaces of the wetting monolayer are correlated.