We propose a simple and effective scheme for the modification of the walls of microfluidic channels fabricated in polycarbonate (PC) after the device has been bonded. The method prevents both static and dynamic wetting of PC by aqueous solutions including viscous, non-Newtonian solutions of polymers as e.g. alginate. The procedure uses dodecylamine, which readily reacts with the carbonate groups of PC to produce a hydrophobic surface. We characterize the dependence of the contact angles and homogeneity of the modified surfaces on the time, temperature, and concentration-all important parameters-of the reaction and provide optimal conditions for the process.