A 3D layered fabrication process based on Multilevel imprint lithography (MIL) is proposed and the critical issues involving template fabrication and overlay accuracy were investigated. A fast and low-cost template fabrication process based on glass wet etching is introduced, in which, the etching mask of Cr metal film is partially remained on top of the template pattern protrusion after etching, which facilitates the residual resist removal and pattern quality improvement. An imprint tool with an alignment subsystem based on computer micro-vision is developed and the experimental results show an average overlay accuracy within 1.5 mu m with a standard deviation within 0.33 mu m. Finally, as an instance of the proposed method, the process based on MIL, electroplating and liftoff was investigated and tri-layer metallic structures with a pattern feature size of 20 mu m were fabricated using the optimized process, which demonstrates the feasibility of the layered fabrication method.