Micro pattern on PDMS surface has been achieved by using synchrotron radiation (SR) stimulated etching. The experimental results indicated that SR stimulated etching has many advantages, such as extremely high etching rate (as large as 40-50 mum per 10 min), area-selectivity and anisotropy at room temperature, high spatial resolution. Combining the SR stimulated etching with photolithography, a PDMS-based microfluidic channel was obtained. The aim of this work is to develop a three-dimensional microfluidic channel with a special through hole, which is beneficial for cell differentiation, functionality and longevity and cannot be fabricated by conventional direct tooling techniques.