Different responses for the front (entrance) and the rear (exit) surfaces of fused silica processed with femtosecond laser pulses at 807 nm were observed under tight focusing conditions (NA = 0.4). The morphology of the surface in the beam path is highly sensitive to the focus position. By adjusting the focus position, we can produce not only a submicrometer cavity but also a submicrometer bubble. We achieved higher-quality micromachining and a better spatial resolution (400 nm) by focusing the laser beam at the rear surface rather than at the front surface.