The fabrication of three-dimensional (3D) structures was demonstrated by proton beam writing (PBW) using a MeV light-ion microbeam system at Japan Atomic Energy Agency. The fabrication of the 3D structures was performed using PBW in a thick SU-8 layer with a thickness of up to 50 mu m, which is a typical negative resist. The authors exposed the negative resist on a silicon substrate to focused MeV proton beams within 1 mu m in diameter, using two different beam energies to obtain two different depths in the resist aiming at fabrication of 3D structures. The two different beam energies were obtained using a 75 mu m Kapton film as a beam energy degrader to generate 1.6 MeV proton beam from 3.0 MeV, or using the accelerator voltage control in order to produce beam energy of 1.2 MeV. The 3D lines and space structures with the same shape were fabricated using the two different methods. An Arc de Triomphe shape was also manufactured to demonstrate the superior and unique features of the PBW as a versatile tool for deep micromachining for 3D structures with high aspect ratio. (c) 2007 American Vacuum Society.