A permanent growth of the thin-film electronics market stimulates the development of versatile technologies for patterning thin-film materials on flexible substrates. High repetition rate lasers with a short pulse duration offer new possibilities for high efficiency structuring of conducting, semi-conducting and isolating films. Lasers with the picosecond pulse duration were applied in structuring the complex multilayered Cu(InGa)Se2 (CIGS) solar cells deposited on the polyimide substrate. The wavelength of laser radiation was adjusted depending on optical properties both of the film and the substrate. A narrow processing window of laser fluence and pulse overlap was estimated with both 1064 nm and 355 nm irradiation to remove the molybdenum backcontact off the substrate. The selective removal of ITO, ZnO and CIGS layers was achieved with 355 nm irradiation in the multilayer structure of CIGS without significant damage to the underneath layers. Use of the flat-top laser beam profile should prevent inhomogeneity in ablation. The EDS analysis did not show residues of molybdenum projected onto the walls of ablated channel due to melt extrusion. Processing with picosecond lasers should not cause degradation of photo-electrical properties of the solar cells but verification is required.