Optimization of laser parameters is a challenge in case of microvia drilling. It is even more complicated to find the right parameters for large area scanning, where not only pulse energy and burst play important roles but also pulse repetition rate, scanning speed and overlap. In case of selective material removal the above process parameters define the amount of the ablated material (etch depth) and the processing time. This paper describes results of experiments carried out to find correlation between the process parameters and the quantity of the ablated material. Flexible polyimide substrates of different thicknesses were processed by frequency trippled, Q-switched Nd:YAG laser. The samples were examined by surface profiler and their cross-sections by optical microscope. The experiments showed that the amount of the ablated polymer is influenced by the features of the patterned copper layer. Even though there is no direct interaction between the laser beam and the copper layer, the thermal conductivity of the circuit pattern influences the temperature of the processed polymer. Because of this phenomenon there is a need to control the laser processing parameters according to the circuit pattern. The correlations we have found between the process parameters and the etch depth make this controlled laser material removal possible.