The focusing of a 786 nm femtosecond laser beam and a second harmonic at 393 nm with dual axicon optics to the surface of c-Si in a vacuum chamber was performed. We demonstrate the importance of avoiding atmospheric effects in order to form and preserve submicron features associated with laser interactions with the solid surface. A submicron hole was formed at the central spot of the Bessel-Gaussian (BG) beam pattern with the fluence just above the ablation threshold. Pre-ablation features consisted of humps and swells on a scale of similar to 100 nm and were formed through the surface modification fluence at the first fringe position of the BG pattern. Laser modified zones were always associated with periodic ripple structures with low and high spatial frequencies during the early stages of laser irradiation. This observation demonstrates the role of the ripple formation in commencing the surface removal processes. Hump and ripple formation mechanisms are considered with respect to volume expansion of the amorphous layer and a conventional model involving the surface electromagnetic wave by taking into account the transient refractive index. (C) 2012 Elsevier B. V. All rights reserved.