AbstractSummary: In the last 10–15 years laser ablation became very popular for the analysis of solid samples. The study of laser‐matter interaction processes on different time scales – nano, pico, femto, and their application in different fields developed a thorough knowledge of the fundamental laws involved in this process. The intention in the current research was to determine the general features of different ablation processes (ns, fs) and ion beam desorption process. The aim was to perform a complete set of measurements of different target materials by means of mass spectrometry studies. More specifically, the mass spectra of ablated and sputtered particles from organic matter were studied. Time of flight mass spectrometer was used for detection. An investigation of the mechanism of laser ablation of biological tissue is a complicated problem due to the complexity of the examined organic material. In our experiments the main aim was to obtain optimal signal detection without the onset of considerable fragmentation. Comparison will be made between the mass spectra from biological samples obtained with laser ablation, and those obtained under bombardment with 9 keV‐accelerated Xe+ ions. As a general tendency in nanosecond ablation and in SIMS experiments the detection of higher mass molecular species is negligible in correspondence to femtosecond laser ablation mass spectra. This can be due to the process of heating that develops under ion bombardment. This work demonstrates the sensitivity of the TOF technique and the potential of using this method for exploring the dynamics of the laser ablation and ion beam desorption processes.An example of 20 µm holes drilled into vascular transplant‐grafts by 30 fs pulses.imageAn example of 20 µm holes drilled into vascular transplant‐grafts by 30 fs pulses.