Highly ordered block copolymer thin films have been studied extensively during the last years because they afford versatile self-assembled morphologies via a bottom-up approach. They promise to be used in applications such as polymeric membranes or templates for nanostructured materials. Among the block copolymer structures, perpendicular cylinders have received strong attention due to their ability to fabricate highly ordered nanopores and nanowires. Nanopores can be created from a thin block copolymer film upon the removal of one block by selective etching or by dissolution of one polymer block. Here we demonstrate the utilization of polystyrene-block-poly(ethylene oxide) diblock copolymer (PS-hv-PEO) with an ortho-nitrobenzyl ester (ONB) as the photocleavable block-linker to create highly ordered thin films. Removal of the PEO block by choosing an appropriate solvent upon photocleavage is expected to yield arrays of nanopores decorated with functional groups, thus lending itself to adsorption or filtration uses. While the feasibility of this approach has been demonstrated, it is crucial to understand the influence of removal conditions (i.e., efficiency of photocleavage as well as best washing solvent) and to evaluate changes in the surface topology and inner structure upon photocleavage. To this end, the time dependence evolution of the surface morphology of block copolymer thin films was studied using grazing-incidence small-angle X-ray scattering (GISAXS) technique in combination with scanning probe microscopy.