In this paper, we report on the development of a rapid prototyping technique for thermoplastic microstructures. In particular, this technology is unique in that it has realized a process that can simultaneously form structures ranging from several tens of micrometers to several millimeters in size, which is often required for microfluidic devices. The key technologies in achieving this are the creation of millimeter-scale mold masters by our original wax reflow process and the creation of hot-embossed molds by a two-step casting process. As a result of prototyping, the molding of microfluidic structures with widths ranging from 50 to 500 µm and reagent reservoir shapes with sizes of several millimeters have been realized. In this process, double casting is a special part of this method of realizing multiscale molds. This effect caused some accuracy degradation due to swelling when casting polydimethylsiloxane (PDMS) daughter molds from PDMS mother molds. This effect was only a 3–9 % decrease in the channel cross-sectional area relative to the mold master, as determined by quantitative evaluation. As described above, the proposed process is a promising technology for the rapid prototyping of thermoplastic products, and is required in the research and development of microfluidic devices at a stage close to practical application.