When the femtosecond laser focused in the water, the breakdown will be induced. The generated highspeed jet and shock wave can be used to etch silica glass for fabricating three-dimensional (3D) microfluidic chips. We present a simple and practical method to produce 3D multilayer microfluidic chips in silica glass. This method offers high design flexibility and fabricating feasibility. We also introduce a convenient cleaning method for diluting and ejecting the ablated debris from microchannel. Therefore, the femtosecond laser induced high-speed jet and shock wave can be used to fabricate complex microfluidic chips in silica glass. Experimental results show that the diameter of microchannel is uniform and the complexity of the microfluidic chip is under control. As a proof of principle, we demonstrate the feasibility of the fabricating process by using the water-assisted femtosecond laser ablation. Crown Copyright (C) 2013 Published by Elsevier B. V. All rights reserved.