A method for characterizing structures etched in a substrate, such as a wafer is disclosed. A bottom of the structure is embedded in the substrate, the substrate having a top side in which the structures are etched and a bottom side opposite to the top side. The method includes the following steps: illuminating the bottom of at least one structure with an illumination beam issued from a light source emitting light with a wavelength adapted to be transmitted through the substrate, acquiring, with an imaging device positioned on the bottom side of said substrate, at least one image of a bottom of the at least one structure through the substrate, and measuring at least one data, called lateral data, relating to a lateral dimension of the bottom of the at least one HAR structure from the at least one acquired image. A system implementing such a method is also disclosed.