Polymer surface patterning and modification at the micro/nano scale has been discovered with great impact in applications such as microfluidics and biomedical technologies. We propose a highly efficient fabricating strategy, to achieve a functional polymer surface, which has control over the surface roughness. The key development in this fabrication method is the polymer positive diffusion effect (PDE) for an ion-bombarded polymeric hybrid surface through focused ion beam (FIB) technology. The PDE is theoretically explored by introducing a positive diffusion term into the classic theory. The conductivity-induced PDE constant is discussed as functions of substrates conductivity, ion energy and flux. The theoretical results agree well with the experiential results on the conductivity-induced PDE, and thus yield good control over roughness and patterning milling depth on the fabricated surface. Moreover, we demonstrate a controllable surface wettability in hydrophobic and superhydrophobic surfaces (contact angles (CA) range from 108.3° to 150.8°) with different CA hysteresis values ranging from 31.4° to 8.3°.