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A novel fabrication process using a hot embossing technique has been developed for micromechanical passive alignment of polymer planar lightwave circuit (PLC) devices. With only one step of embossing, single-mode waveguide straight channels and micropedestals for passive aligning are simultaneously defined on a polymer thin film with an accuracy of ±0.5 μm. This process reduces the steps for fabricating alignment structures. A fabricated polymer PLC chip and fibers are combined on a v-grooved silicon optical bench (SiOB) in a flip-chip manner. The process provides a coupling loss as low as 0.67 dB per coupling face and a cost-effective packaging solution for various polymer PLC devices.