We have used digital holographic tomography (DHT) to study the refractive index (density) changes occurring under Vickers indentations in silica, soda-lime, and non-alkaline aluminoborosilicate glasses. The measurements confirm that the maximum refractive index (density) is not constant but increases with load up to 300 gf. At higher loads (500 gf and 1 kgf), a subsurface (median) crack in soda-lime glass is observed with no apparent surface trace. The appearance of this crack reduces the maximum refractive index (density) observed. In addition, the vertical cross section of the 3D refractive index (density) map has been successfully obtained using a square fiber sample and lateral observation. These results clearly demonstrate a promising potential of DHT to evaluate the shape and the density distribution of the structurally modified zone in a Vickers-indented glass.