A process for producing a fluorocarbon microstructure capable of easily fabricating a three-dimensional fluorocarbon microstructure. The process for producing a fluorocarbon microstructure comprises a first processing step for forming, on a substrate (2), a film deposition portion with a given pattern made up of a through-hole figure by etching the substrate (2), a fabricating step for forming a fluorocarbon film (6) on an inner circumferential surface of a film deposition portion (9) to fabricate a fluorocarbon region surrounded by the fluorocarbon film (6), and a second processing step for fabricating the fluorocarbon microstructure protruding from a processing surface of the substrate (2) by etching a given region other than a fluorocarbon region on the substrate (2). Hence, the three-dimensional fluorocarbon microstructure can be fabricated which comprises a complicated structure that has conventionally been hard to fabricate. Thus, a microchannel (1) equipped with the three-dimensional fluorocarbon microstructure can be easily fabricated.