Solvent vapor annealing is shown to be a useful technique for controlling the formation of poly(isoprene-b-styrene) (PI-b-PS) block copolymer thin film nanostructures. Annealing in methyl ethyl ketone (MEK) solvent vapor yields a hexagonal-type structure (78 nm repeat distance), while toluene yields a fingerprint texture. Solvent choice for spin coating dramatically changes the initial order in these films: MEK provides a useful hexagonal structure without annealing, while toluene yields a disordered nanostructure. N-octadecyltriethoxysilane is used to form a low surface energy self-assembled monolayer which effectively reduces pinning of the copolymer to the substrate, allowing the development of regions (similar to 1 mu m in diameter) with a high degree of hexagonal order. However, after several hours of annealing in MEK vapor, the copolymer ultimately dewets from the surface. Contact mode scanning probe microscopy has proven itself to be a very useful tool for imaging the nanostructures, without damaging the films. Friction mode provides high contrast images of PI-b-PS nanostructures, suggesting the lack of a wetting layer in the solvent vapor annealed films. (c) 2005 American Vacuum Society.