The accuracy and clogging of microchannels are important for assessing the quality of
lab on chip (L-O-C) devices. The clogging affects the fluid mixing efficiency and influences the
bonding of substrate. In this paper, inexpensive and quick method for microchannel fabrication in
polymethyl methacrylate (PMMA) while reducing the thermal damage is introduced. Accordingly,
the substrate was covered with a thin layer of water during CO2 laser ablation. The effect of water
cooling on the clogging formation, heat affected zone and the microchannel geometry in terms of
depth and width is investigated. Clogging formation mechanism in the intersection of Y-channel is
studied to improve its quality for microfluidics applications. During the experimental work, the CO2
laser power was varied from 2.4 to 6 W at scanning speed from 5 to 12.5 mm/s. The results showed
that covering the PMMA substrate with a thin layer of water prevented clogging formation and
reduced the heat affected zone.