Polymer materials have been utilized in microfluidic devices because of their properties and competitive cost for single-use devices. However, most microfabrication processes can not produce true three dimensional features in polymers. In this study, a new method with lost-wax casting was proposed to fabricate three dimensional microstructures in polymer-based microchannels. A feasibility study was conducted with epoxy and paraffin wax sacrifice. The microchannel with both-end fixed horizontal rods was produced with precise dimension. This structure is not possible to be fabricated by other replicating methods such as hot embossing or casting. The proposed lost-wax casting process is expected to advance the development of three dimensional polymer-based microchips for both the experimental research in laboratory and the mass production in industry.