Highly ordered nanopore arrays were successfully fabricated using poly(ethylene oxide) (PEO) and polymethacrylate with azobenzene mesogen in side chains [PMA(Az)] block copolymer film based on irradiation of 172-nm vacuum ultraviolet (VUV) light. The block copolymer forms a highly ordered microphase-separated film with perpendicularly oriented PEO cylinders just by thermal annealing through a self-assembling process. We found that the etching rate of the PEO homopolymer was much higher than that of the PMA(Az) homopolymer at a chamber pressure of 102 Pa of atmosphere under VUV irradiation. The etching rate of the PEO component in the two systems of microphase separation and macrophase separation of the homopolymer blend crucially depended on the feature size of phase separation. In the PEO selective etching process of the block copolymer film, the water-contact angle of the film dramatically increased due to elimination of hydrophilic PEO. The resulting nanopore array film will be useful for low-density target materials.