Thin films of the biopolymers gelatine and chitosan were treated using femtosecond pulse shaping techniques combined with a microscope-based setup for material processing. The polymer films were irradiated with laser pulses of 35 fs and a central wavelength of 790 nm provided by an amplified Ti:Sapphire system. The effect of temporal pulse shaping, with quadratic and cubic spectral phases, on the induced morphology was analyzed by characterization of the created surface structures via scanning electron microscopy. We observed different material modification thresholds and different structure sizes for temporally asymmetric pulse shapes. The results indicate the possibility of control of the generated microstructures and are discussed in relation to the formation of free electrons and the different contributions of multi-photon and avalanche ionization processes. (C) 2013 Elsevier B.V. All rights reserved.