By laser-micromachining from the rear surface that is in contact with distilled water, we can directly produce Three-dimensional micro-holes in silica glass. The micro-holes have the constant diameters of several microns and the high aspect ratios. In this paper, we present the morphological characteristics of the micro-hole. Femtosecond laser pulses (130-fs, 800 nm, 1-kHz) generated from an amplified Ti:sapphire laser were first focused onto the rear surface of the silica glass with the thickness of 1 mm by a 0.55-numerical aperture microscope objective. After 48 sequential pulses were launched into the sample, we moved the focal spot by a step of 1 micron toward the front surface. We fabricated micro-holes with the diameter of 4 - 8 microns by repeating the irradiation and the movement. We observed the morphology of the hole and the debris generated by the laser ablation. We also analyzed the capillary phenomenon in the dead-end micro-holes. We found two phases in the rising of the distilled water: the first phase occurred very fast within 0.1s and second phase was slow. This result agrees with the previous result [N.P. Migoun, et al., Proc. 15th WCNDT, Roma(2000)] that used a glass capillary tube.