In the last years more and more effort has been put into the development of thin-film organic solar cells using conductive and semi-conductive polymers. A great advantage of these polymers is the possibility to deposit them in high throughput print and coating processes. This feature provides huge potential for future production of low cost photovoltaics. While TCO layers form the transparent front contact, polymers are used for the buildup of the active layer and the design of the interface between active layer and front contact. The polymer materials have to be patterned in order to allow for a row connection of the solar cell work (typically by structured deposition, e.g. printing). In addition the bulk hetero junction (BHJ) of the active layer consisting of poly(3-hexylthiophene):phenyl-C61-butyric acid methyl ester (P3HT:PCBM) requires an annealing step to optimize the layers structure and therewith the efficiency of the solar cell (typically by thermal treatment, e.g. oven). 3D-Micromac used ultra-short pulsed lasers to evaluate the applicability of various wavelengths for the selective ablation of the BHJ consisting of P3HT:PCBM on top of a Poly(3,4-ethylenedioxythiophene) poly(styrenesulfonate) (PEDOT:PSS) and indium tin oxide (ITO) film system on glass substrates. The process of laser annealing was investigated using a short-pulsed laser with a wavelength close to the absorption maxima of the BHJ.