AbstractPhase separation occurs in thin films of polymer blends when molecular mobility is promoted by a temperature above the glass transition but inside the twophase region (temperature quench), or a common solvent added to the polymers (solvent quench). This phenomenon can be altered by a homogeneous surface or pre-patterned substrate, resulting, e.g., in self-stratification or pattern replication, respectively. Such self-organisation processes ordering polymer phases were observed for model polymer blends (deuterated/hydrogenated polystyrene, dPS/hPS, and deuterated/partially brominated PS, dPS/PBrS, both with hPSpolyisoprene diblocks added; dPS/poly(vinylpyridine) and PBrS/PVP) with highresolution ion beam techniques (Nuclear Reaction Analysis, profiling and mapping mode of dynamic Secondary Ion Mass Spectrometry) and Atomic Force Microscopy. The self-stratification process is strongly affected by both the range as well as the strength of the surface/polymer interactions. This is illustrated for the temperature-quenched blends with surface-active copolymer additives tuning the interactions exerted by both external surfaces. The pattern transfer from the substrate to the films is demonstrated for the solvent-quenched blends. Patterndirected composition variations (SIMS maps) coincide with free surface undulations (AFM images). The most effective pattern replication is achieved for the length scale of phase domain morphology comparable with the pattern periodicity and for carefully adjusted polymer/substrate interactions.