In this study, we fabricated three-dimensional (3-D) polytetrafluoroethylene (PTFE) microstructures using the plane-pattern to cross-section transfer (PCT) method with synchrotron radiation (SR) ablation. We found that the etching rate increased with increasing SR exposure. This was attributed to the heating of the PTFE surface as evidenced by the emission of fluorocarbon gas from the surface. Using the PCT method, we successfully produced various 3-D PTFE microstructure shapes by varying the energy distribution of the SR exposure using multiple scanning speeds.