We demonstrate self-fabrication of a submicrometer-sized void array in fused silica using a 100 fs 0.2–3 μJ Ti:Sapphire femtosecond laser and a high 0.9 numerical aperture (NA) objective lens. The effect of the focusing conditions of NA, laser energy, and pulse number on the shape of the fabricated void was investigated. The void has a linearly drawn shape in the direction of the laser irradiation when a single pulse is irradiated and an increasing number of incident pulses resulted in the break up of the long void into multiple spherical ones, leading to a periodically aligned void array. The void shape also varied with the depth of the focus point beneath the fused silica surface, because the amount of self-focusing has a significant effect on the generation of the voids. The void shape was narrower and longer when the laser pulse was focused with the higher NA (up to 0.9) objective lens in the deeper position (up to 70 μm) in the fused silica.