Two-photon polymerization technology has been used to fabricate submicrometer three-dimensional (3D) structures using a new polyfunctional perfluoropolyether-based resist, which is a polymer intrinsically hydro-phobic and chemically resistant. The fluorinated resist was designed and synthesized in this work and successfully employed to fabricate woodpile structures in various experimental conditions. This is the first demonstration of the capability to fabricate hydrophobic and chemically resistant 3D structures with submicrometer resolution and arbitrary geometry.