High repetition rated femtosecond laser oscillator systems with low pulse energy are more often applied for precise and safer eye surgery. Especially, the cutting procedure in the crystalline lens is of high important for presbyopia treatment. Nevertheless, the fundamental laser tissue interaction process is not completely understood, because apparently a self-induced process takes place, were one modified region changes the focusing behavior of following laser pulses. We used a MHz repetition rate femtosecond laser system with nJ-pulse energy which were focused inside an ocular-tissue-phantom (Hydroxy-ethylmethacrylat - HEMA) to induce photodisruption. The material change, caused by the fs-pulses was measured simultaneously with a compact digital-holographic microscope. To investigate the material manipulation at different time scales, we used a continuously illuminating light source. The holographic images provide quantitative values for optical path length difference (OPL), which is equivalent to a refractive index change. This change of the optical properties may cause following pulses to obtain different focusing conditions. Time lapse measurements during the laser application were performed, which show the temporal evolution of OPL. An increase of OPL during the laser application was measured, which was followed by a decrease in OPL after laser processing. Furthermore, similar experiments were performed in distilled water and in native porcine crystalline lenses. The fs-laser cutting effects in HEMA and crystalline lens were transferable. Simultaneous measurements of the material modification during the cutting process give rise to better knowledge of treatment modalities during ocular tissue processing.