Performing large-scale atomic simulations by means of kinetic Monte Carlo method we study room temperature self-organization of 3d magnetic atoms (Fe, Co) on fcc (110), Cu (110) in the sub-monolayer regime. The energetics of various diffusion processes relevant for these systems is investigated based on first principles calculations. We reveal that surface-confined atomic intermixing plays a significant role in the formation of nanostructures. Our results lead to the conclusion that the deposited species (Fe, Co) are captured into the topmost surface layer, while the ad-layer structure consists mainly of the expelled substrate atoms (Pd, Cu). Our studies shed a light on recent experimental investigations on the metal-on-metal growth on fcc (110) surfaces.