The large intensities available with femtosecond (fs) laser pulses allow permanent structural modifications in transparent materials with high spatial resolution. Irradiation of self-standing transparent biopolymer films, such as collagen, pure and curcumin doped gelatine employing a 60-fs high-power 11 MHz Ti-Sapphire oscillator laser system linked to an optical microscope led to modifications and ablation. Swelling modifications consisting in the foaming of the irradiated area and formation of a single layer of bubbles arranged around the narrow ablation crater were investigated by optical, scanning force (SFM) and scanning electron (SEM) microscopy. These modifications occur at fluences below the respective ablation thresholds, i.e. ablation processes take place on modified swelled phases. The results are discussed in terms of local temperature increase, generation of thermoelastic stress, physico-chemical effects, and in terms of an incubation model, i.e. the accumulation of these phenomena upon successive pulse irradiation.