The effects of the molecular weight of polystyrene (PS) component on the phase separation of PS/poly(4-vinylpyridine) (PS/P4VP) blend films on homogeneous alkanethiol self-assembled monolayer (SAM) and heterogeneous SAM/Au substrates have been investigated by means of atomic force microscopy (AFM). For the PS (22.4k)/P4VP (60k) system, owing to the molecular weight of PS component is relatively small, the well-aligned PS and P4VP stripes with good thermal stability are directed by the patterned SAM/Au surfaces. With the increase of the molecular weight of PS component (for the PS (582k)/P4VP (60k) system), the diffusion of P4VP is hindered by the high viscosity of PS during the fast spin-coating process. The phase separation behavior of PS/P4VP on the SAM/Au patterned substrates is similar to that on the homoueneous SAM and cannot be easily directed by the patterned SAM surfaces even though the characteristic length of the lateral domain morphology is commensurate with the stripe width. This indicates that the relative viscosity of the PS is one of the dominant factors in obtaining well-aligned pattern by the phase separation of polymer blends. (C) 2004 Published by Elsevier Ltd.