Scanning transmission electron microscopy was carried out to study the three-dimensional microstructures of periodic strained layers induced by the irradiation of femtosecond laser pulses inside a silicon carbide single crystal. The cross section of laser-irradiated line consisted of a shell-shaped modified region surrounding a core region with no modification. The laser-modified region was composed of strained layers with a typical spacing of 200 nm. Nanovoids from 10 nm to 20 nm in diameter were observed. Three-dimensional tomographic images clearly show the plate-like shape of strained layers extending parallel to the electric field of the laser light and the random distribution of nanovoids in the strained layers. The three-dimensional observation provides insight into the formation mechanisms of periodic microstructures.