The orientation of the lamellae formed by the phase separation of symmetric diblock copolymer thin films is strongly affected by the wetting properties of the polymer blocks with respect to the substrate. On bare silicon wafers the lamellae of polystyrene-b-polymethylmethacrylate thin films tend to order parallel to the wafer surface, with the polymethylmethacrylate block preferentially wetting silicon. We have developed a methodology for inducing the arrangement of lamellae perpendicular to the substrate by using chemically modified substrates. This is done by chemisorbing a self-assembled monolayer of thiol-terminated alkane chains on thin gold films deposited on silicon wafers. We also show that it is possible to spatially control the perpendicular orientation of the lamellae at sub-micron length scales by using simple chemical patterns and etch them, in order to produce nanolithographic templates. This method may be of great technological interest for the preparation of well-defined templates using block copolymer thin films.