We experimentally examined the effect of laser energy fluence on the ablation of a silicon wafer using a Ti:sapphire femtosecond laser system. A femtosecond laser was focused through an oxide-metal-oxide (Al2O 3/Al/Al2O3) film engraved with a subwavelength annular aperture (SAA) structure, i.e., a Bessel beam composed of a femtosecond laser created using a SAA. The optical performance, such as depth-of-focus (DOF) and focal spot of the SAA structure, was simulated using finite-difference time domain (FDTD) calculations. We found that a far-field laser beam propagating through the SAA structure possesses a sub-micron focal spot as well as high focus intensity. The experimental results demonstrated that silicon can be ablated using an input ablation threshold of an order of 0.05 J/cm2 with a pulse duration at around 120fs. We found the obtained surface hole to have a diameter smaller than 1μm. Different surface ablation results obtained by using different threshold fluences of input laser energy are shown. Possible applications of this technique includes executing high aspect ratio laser drilling for thin film microfabrication undertaking thru silicon via (TSV) for 3DIC, etc.