On the basis of the major application for block copolymers to use them as separation membranes, lithographic mask, and as templates, the preparation of highly oriented nanoporous thin films requires the selective removal of the minor phase from the pores. In the scope of this study, thin film of polystyrene-block-poly(ethylene oxide) block copolymer with a photocleavable junction groups based on ortho-nitrobenzylester (ONB) (PS-hν-PEO) was papered via the spin coating technique followed by solvent annealing to obtain highly-ordered cylindrical domains. The polymer blocks are cleaved by means of a mild UV exposure and then the pore material is washed out of the polymer film by ultra-pure water resulting in arrays of nanoporous thin films to remove one block. The removal of the PEO materials from the pores was proven using the grazing-incidence small-angle X-ray scattering (GISAXS) technique. The treatment of the polymer film during the washing process was observed in real time after two different UV exposure time (1 and 4 h) in order to draw conclusions regarding the dynamics of the removal process. In-situ X-ray reflectivity measurements provide statistically significant information about the change in the layer thickness as well as the roughness and electron density of the polymer film during pore formation. 4 H UV exposure was found to be more efficient for PEO cleavage. By in-situ SFM measurements, the structure of the ultra-thin block copolymer films was also analysed and, thus, the kinetics of the washing process was elaborated. The results from both measurements confirmed that the washing procedure induces irreversible change in morphology to the surface of the thin film.