Direct-write laser processing has been demonstrated to be capable of both surface patterning of micro- and nanoscale structures on polymer surfaces without significant modification of the surface chemistry or optical transmission of the laser processed area. In this work, the creation of microchannels via direct-write laser processing of 188 μm thickness cyclic olefin polymers is demonstrated, along with a route towards channel functionalization. Cyclic olefin polymers (COP) are an emerging class of polymers noted for their high chemical resistance, biocompatibility and higher optical transparency when compared to other common polymers. These properties make them excellent substrates for the fabrication of microfluidic devices. This paper presents the first investigation into infrared laser processing of COP using a 1064 nm Nd:YAG laser. Scanning electron microscopy and Raman spectroscopy were utilized to investigate the morphology and composition of these laser textured surfaces. A route for functionalization of these substrates for chemical and biological speciation and separation was examined using carbon nanoparticles. The nanoparticles were produced using pulsed laser ablation in liquid (PLAL) which has been reported as a fast and adaptable method for nanoparticle production. The nanoparticles produced were using transmission electron microscopy while the coating of substrates with these CNPs was examined using SEM. These results are discussed in the context of development of a new route for achieving surfaces optimized for microfluidicbased separations and speciation.