Prism-coupling systems and methods for characterizing large depth-of-layer waveguides formed in glass substrates are disclosed. One method includes making a first measurement after a first ion-exchange process that forms a deep region and then performing a second measurement after a second ion-exchange process that forms a shallow region. Light-blocking features are arranged relative to the prism to produce a mode spectrum where the contrast of the mode lines for the strongly coupled low-order modes is improved at the expense of loss of resolution for measuring characteristics of the shallow region. Standard techniques for determining the compressive stress, the depth of layer or the tensile strength of the shallow region are then employed. A second measurement can be made using a near-IR wavelength to measure characteristics of the deeper, first ion-exchange process. Systems and methods of measuring ion-exchanged samples using shape control are also disclosed.