Femtosecond laser ablation technique has been used to process Si and Au targets in vacuum, air and water environment. The threshold of ablation was found to be much lower for Si compared to Au and that was related to much better radiation absorption of Si. The values of the threshold were almost identical for vacuum, air and water in the case of Si (0.4 J/cm2 0.2 J/cm2 in the single and multi-pulse irradiation regime, respectively) and Au (0.9 J/cm2 and 0.3 J/cm2). Craters on the surface of Si and Au were essentially similar for low fluences, suggesting an involvement of the same radiation-related mechanism of material removal, whereas for high fluences significant differences could take place. In particular, quite different crater morphologies were observed during the laser ablation in water, including ones with nanoporous layers for Si and ones with concentric spheres for Au. The differences of morphologies for high laser fluences were explained by the involvement of plasma-related effects under the processing in relatively dense media.© (2004) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.