Poly(methyl methacrylate)(PMMA) and Poly L-lactic acid (PLLA) are transparent and they are suitable for optical purposes. The multi-layer polymer microfabrication can be applied for a large displacement actuator and precision sensors. A new method is intruduced to generate the multi-layer polymers microstructures by X-ray lithography with alignment. The function of X-ray on polymer materials are breaking the polymer main chain and generating intermediates which can be degraded further and finally dissolved by the solvent interaction. The method for polymer micromachining by using X-ray lithography with alignment for fabrication multi-layer micro polymer structures is confirmed experimentatively.