Utilizing the near-field enhancement effect of a polystyrene microsphere, direct ablation of nanohole arrays by a temporal-shaping femtosecond (fs) laser pulse is presented. The nanohole arrays, which are circular, regular, and free of cracks, were processed without extra post-processing, and their average diameter decreased gradually, as the double-pulse delay increased until 2500 fs. The simulated results by a plasma model and finite difference time domain solution demonstrate that the size decrease of the structure is attributed to the increase of the ablation threshold of silicon. Through fs laser near-field fabrication, the FWHM of nanoholes can be reduced to approximately 50 nm (λ/16) and even to 23 nm when using the second harmonic laser at a wavelength of 400 nm.