We propose a method for the modification of surfaces of microchannels in chips fabricated in polycarbonate (PC) that makes the devices resistant to a range of organic solvents. Coating of PC with branched polyethyleneimine (BPEI) with the use of trimethylpropane triglycidyl ether (TTE) as a linker renders the devices resistant to toluene, benzene, acetonitrile, tetrahydrofuran, dioxane and ethylene dichloride. The optimized procedure of modification allows for continuous operation of the chips for several hours without dissolution of PC. Additional modification with the use of Krytox® allows for the use of Fluorinert (FC-40) as the continuous phase and for generation and handling of droplets of organic solvents that are miscible with water.