Nanofabrication of three-dimensional (3D) structures with a high aspect ratio has been achieved using electron-beam (EB) lithography. Although electron scattering, or the proximity effect, on the remaining parts in positive resist is generally serious for repeated EB writing from different 3D directions, we can largely avoid the effect by adding appropriate surrounding buffer regions, which are cut off by the following EB writing and development. This enables us to make a 3D nanostructure in poly(methyl methacrylate) (PMMA), which demonstrates the great structural flexibility obtainable in our EB technique.