Self-assembling polymers have recently attracted significant scientific interest, since they spontaneously generate highly ordered structures with high resolution precision, and provide simple, parallel, and cost-effective processes for nanofabrication. Such systems can be achieved with block copolymers which, when produced as thin films, offer great potential as lithographic templates for the fabrication of photonic band-gap materials, ultrahigh-density nanodots or nanowire arrays, memory and capacitor devices, and nano-patterned substrates for biosensors. Although self-assembling block copolymers can form a variety of surface topographies at the nm scale, like spheres, cylinders, and lamellae, their structural steering through the annealing conditions has in many cases not been fully investigated. In the present investigation optimum production conditions for the preparation of nanostructures from poly(styrene)-block-poly(MMA) diblock copolymers have been established to enable the production of surfaces as thin films (<40 nm) on spin-coated silicon wafers either with parallel cylindrical structures or with vertical cylinders. The resulting self-assembling structures were then evaluated by atomic force microscopy. The obtained nanostructured polymers were then incubated with two microbial species, the gram negative E. coli and the gram positive S. aureus to assess their behaviour. The patterns of the thin film surfaces affected the bacterial attachment. Such self assembly processes can be used to create surfaces acting as bacterial attractants or repellents.