We report on an optimization study of percussion drilling thin metal sheets employing a high repetition rate, high power femtosecond laser with respect to the resulting heat accumulation. A specified simplex algorithm was employed to optimize the spatial drilling sequence, whereas a simplified thermal simulation using COMSOL was validated by comparing its results to the temperature measurements using an infrared camera. Optimization for drilling borehole matrices was aspired with respect to the generated temperature across the processed specimen, while the drilling strategy was altered in its spatial drilling sequence and by using multi-spot approaches generated by a spatial light modulator. As a result, we found that an optimization strategy based on limited consecutive holes in a Moore neighborhood led to reduced temperatures and the shortest process times.