This manuscript presents a study of physical and chemical properties of microchannels fabricated by femtosecond laser processing technology in thermoplastic polymeric materials, including poly(methyl methacrylate) (PMMA), polystyrene (PS) and cyclic olefin polymer (COP). By surface electron microscopy and optical profilometry, the dimensions of microchannels in the polymers were found to be easily tunable, with surface roughness values comparable to those obtained by standard prototyping techniques such as micromilling. Through colorimetric analysis and optical microscopy, PMMA was found to remain nearly transparent after ablation while COP and PS darkened significantly. Using infrared spectroscopy, the darkening in PS and COP was attributed to significant oxidation and dehydrogenation during laser ablation, unlike PMMA, which was found to degrade by a thermal depolymerization process. The more stable molecular structure of PMMA makes it the most viable thermoplastic polymer for femtosecond laser fabrication of microfluidic channels.