We recently developed a microfabrication technique [microfabrication using laser-induced bubble (microFLIB)] and applied it to polydimethylsiloxane (PDMS), a thermoset polymer. The technique enabled the rapid fabrication of a microchannel on a PDMS substrate and selective metallization of the channel via subsequent plating; however, the technique was limited to surface microfabrication. Therefore, we explored the feasibility of three-dimensional (3D) microFLIB of PDMS using a nanosecond laser. In the experiment, a laser beam was focused inside pre-curing liquid PDMS and was scanned both perpendicular and parallel to the laser-beam axis to generate a 3D line of laser-induced bubbles. In the microFLIB processing, the shape of the created bubbles was retained in the pre-curing PDMS for more than 24 h; thus, the line of bubbles generated by the perpendicular laser scanning successfully produced a 3D hollow transverse microchannel inside the PDMS substrate after subsequent thermal curing. In addition, a through-hole with an aspect ratio greater than ∼200 was easily fabricated in the PDMS substrate by parallel laser scanning. The fabrication of a 3D microfluidic device comprising two open reservoirs in a PDMS substrate was also demonstrated for biochip applications.