Annealing silicon at high temperatures in hydrogen ambiance has been reported to induce surface diffusion of silicon; in these conditions, adapted 2D arrays of trenches etched in Bulk Si are transformed into buried cavities creating suspended membranes. A 3D nanostructuration of silicon through hard mask engineering and high temperature annealing in hydrogen ambiance is reported. By using a nitride-oxide hard mask stack instead of a sacrificial oxide hard mask for a free surface (maskless) annealing, we open new technological and design possibilities using 2D arrays of various geometry trenches. Implications and potential device applications are discussed.