A poly(isoprene-b-lactide) (PI-b-PLA) polymer forming cylinders of PLA in a PI matrix was examined as a polymer system to generate nanostructured vertical arrays of hexagonally packed cylinders. This investigation was motivated by the favorable properties of PI-b-PLA for fabricating nanoporous materials. Films were swollen and annealed with chloroform over a range of thickness and solvent concentration. Examination of the films after swelling with scanning force microscopy and grazing incidence X-ray scattering showed that films with either parallel or perpendicular domain orientations could be obtained. The domain orientation depends on the selectivity of the film surface, mediated by the concentration of chloroform, and the incommensurability of the polymer domain spacing and the swollen film thickness. The results show that solvent annealing is an effective method for obtaining oriented PI-b-PLA cylinder templates and more generally an effective method for obtaining perpendicularly oriented cylinders over a wide area from an initially unoriented film.