We report a reflow process for forming rounded channels of submillimeter height. In this method, a hot-melt glue comprising primarily of an ethylene–vinyl acetate (EVA) copolymer is patterned onto a substrate via vacuum-assisted micromolding (VAM) in capillaries using polydimethylsiloxane (PDMS) molds. This method enables a submillimeter channel structure to be fabricated using a thermoplastic resin. Subsequently, by heating the mold, rounded cross-sectional channels with a height of 100 µm order can be fabricated, which is difficult to achieve in the conventional reflow process using positive resists. By observing the cross-sectional shape of the reflowed mold, it is confirmed that the cross-sectional shape of the channels can be controlled by changing the heating time. In addition, the method offers flexibility in terms of the channel layout. As an application to microfluidic devices, we fabricate and evaluate a microperistaltic pump comprising three microvalves using a typical hot plate and a small vacuum pump. In addition, the PDMS mold and fabricated glue mold can be used repeatedly. In general, the proposed process is a simple and inexpensive means of fabricating micropumps and valves that can handle large objects such as cell tissues.