We performed ablation studies on multi-layer systems at different wavelength - pulse duration combinations. The multi-layer systems of interest, 150 nm thin indium tin oxide (ITO), 200 thin polyaniline (PANI) on 1 micrometers thick photo resist, and 280 nm PPV/pedot layer-combination on 150 nm thin ITO are optically transparent and used for a variety of industrial applications. One important goal of the study was to determine the possible process window for a complete removal of only the top layer, leaving the remaining layer basically unharmed. The investigations were conducted with the following wavelength - pulse duration combinations: 800 nm and 180 fs, 800 nm and 5 ps, 266 nm and 150 fs, 266 nm and 5 ns, 532 nm and 5 ns. We generated micro dots, lines and areas to determine the damage threshold, the processing quality and the processing speed for the specified application of selective layer removal. The structures were analyzed by means of optical and atomic force microscopy. In some cases, we observed a strong pulse duration dependence in the ablation threshold, an indication for the observed difficulties using laser pulse in the ns range. Comparative studies at different wavelengths demonstrate that laser pulses in the UV are not necessarily always a first choice to achieve a precise removal of the optically transparent top layer.