Microfluidic devices have become increasingly popular in various fields, including biosensors and chemical analysis. Modification of the wetting properties of microchannels offers a wide range of possibilities, from separating aqueous and organic phases to increased mixing and analysis efficiency, and eliminating micropumps in microfluidic chips. In this study, we investigate changes in the wetting properties of microchannels fabricated on Poly methyl methacrylate following laser irradiation. It was found that after re-irradiation of microchannel surface at fluences below the ablation threshold, decreasing the laser fluence and increasing the number of pulses lead to increase the hydrophilicity of the super-hydrophobic microchannel surface formed by laser irradiation at a fluence above the ablation threshold. By altering the irradiation parameters, we fabricated super-hydrophobic and super-hydrophilic channels on the sample. The effective chemical and morphological changes were investigated.