We fabricated a Si based microchannel without cover plates by an Ar/F 2 vapor etching process. In the Ar/F 2 vapor etching process, the Si substrate was etched in proportion to the etching time with good controllability. We succeeded in the transport of Escherichia coli cells in the microchannel. In addition, we fabricated a Si-based two-step microchannel without cover plates by Ar/F 2 vapor etching and Cl 2 -based inductively coupled plasma (ICP) etching processes. The proposed microchannel would be useful for the separation of bacterial cells according to size.