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A simple O2 plasma etching method is developed and first used to fabricate planar nanofluidic channels in thermoplastic polymers. In this process, a copper etching mask with a micron-scale width is made by traditional UV lithography and wet etching on a polymer substrate, then the polymer substrate is etched by O2 plasma in a commonly used plasma cleaner to form the planar nanochannel. Effects of the process parameters of the plasma cleaner on the etching rate are studied. The average etching rate for most thermoplastic polymers used in lab-on-a-chip is about 10 nm/min and the surface roughness is less than 2 nm when radio frequency power and chamber pressure are 60 W and 200 Pa, respectively. To demonstrate this method, a polymethylmethacrylate (PMMA) micro-nanofluidic chip containing nine parallel nanochannels, 100 nm in depth, 5 μm wide and 1 mm long, is fabricated to investigate the ion enrichment of 1 M fluorescein isothiocyanate (FITC) in 10 mM phosphate buffered saline (PBS) buffer.