Suffusion is a process by which fine particles move through the voids between coarse particles (intergranular voids) by seepage flow. Therefore, identifying the arrangement of coarse particles (coarse matrix), intergranular voids, and the spatial distribution of fine particles is a key issue for studying suffusion. Transparent soil is being increasingly used to replace real soil in laboratory model tests for studying the internal particle movements and pore fluid flow in soils. This study established an experimental setup for scanning a transparent soil specimen during seepage by a moving laser and made an attempt to construct a 3D digital mesostructural model of the specimen based on the images of the sequentially illuminated cross-sections. An example test on a gap-graded soil was conducted to show the performance of the presented method. It demonstrated that the coarse matrix and intergranular voids can be visualized and quantified at satisfactory precisions; moreover, the loss and redistribution of fine particles as well as important phenomena such as deposition at pore bodies and clogging of pore throats can also be visualized and identified qualitatively.