Cylindrical nanoporous structures were prepared by using a mixture film of polystyrene-block-poly(methyl methacrylate) copolymer (PS-b-PMMA) and PMMA homopolymer (hPMMA), and they were analyzed by transmission electron microtomography (TEMT), X-ray reflectivity (XR), and grazing incidence small-angle X-ray scattering. For this purpose, the mixture film was spin-coated onto a silicon wafer modified by a neutral brush for PS and PMMA blocks, which generates PMMA cylindrical microdomains oriented normal to the substrate. Two methods were employed to prepare nanoporous structures: (1) all of the PMMA phase (PMMA block and PMMA homopolymer) in the film was removed by UV irradiation, followed by rinsing with a selective solvent (acetic acid) to PMMA and (2) only PMMA homopolymer was removed by selective solvent etching without UV irradiation. We found via TEMT and XR that the nanoporous structure in the film prepared by UV irradiation exhibited almost perfect cylindrical shape throughout the entire film thickness. However, when the film was rinsed with a selective solvent, nanoporous structures were not straight cylinders but had a funnel shape in which the diameter of nanopores located near the top of the film was larger than that located near the bottom of the film.