Surface-enhanced Raman scattering (SERS) has been considered as one of the most promising tools for molecular analysis. To develop practical platforms, a variety of nanoparticles and two-dimensional (2D) nanostructures have been prepared. However, low signal intensity or slow binding kinetics in conventional approaches limits their applications. To overcome these shortcomings, production and usage of three-dimensional (3D) nanostructures remain an important yet unmet need. In this paper, we report novel and effective SERS-active materials by fabricating hierarchically structured SiO2 microcylinders decorated with gold nanoparticles. In order to fully develop 3D nanostructures, while maintaining fast diffusion of analyte molecules, we used self-assembled nanostructures of block-copolymers (BCPs) confined in the microholes of an imprinting mold; the BCPs could provide a template for producing 3D nanostructure composed of nanofibers with sub-100 nm diameter through their rnicrophase separation, whereas imprinting technique provided cylindrical geometry for the local confinement of the BCPs. Microcylinders with nanodomains were then transformed into microcylinders with 3D nanopores via reactive-ion etching and, subsequently, their nanopores were decorated by gold nanoparticles. The resultant 3D nanopores enable a high loading of gold nanoparticles and formation of abundant hot spots and microcylinders facilitate the fast diffusion of analyte molecules through the nanopores, resulting in significant enhancement of SERS intensity.