This paper presents a method for fabrication of microchannels on cyclic olefin polymer films that have application in the field of microfluidics and chemical sensing. Continuous microchannels were fabricated on 188-μm-thick cyclic olefin polymer substrates using a picosecond pulsed 1064 nm Nd:YAG laser. The effect of laser fluence on the microchannel morphology and dimensions was analysed via scanning electron microscopy and optical profilometry. Single laser passes were found to produce v-shaped microchannels with depths ranging from 12 to 48 μm and widths from 44 to 154 μm. The ablation rate during processing was lower than predicted theoretically. Multiple laser passes were applied to examine the ability for finer control over microchannel morphology with channel depths ranging from 22 μm to 77 μm and channel widths from 59 μm to 155 μm. For up to five repeat passes, acceptable reproducibility was found in the produced microchannel morphology. Infrared spectroscopy revealed that the polymer surface chemistry was not significantly altered via the laser ablation process. These results were compared to other work conducted on cyclic olefin polymers.