Carrier activation and end-of-range defect density of ultra-shallow junctions in integrated circuits are determined using modulated optical reflectance signals, DC reflectances of pump or probe laser beams, and in-phase and quadrature signal processing. A method for determining characteristics of an ultra-shallow junction includes periodically exciting a region of the substrate using a pump laser beam, and reflecting a probe laser beam from the excited region. A modulated optical reflectance signal is measured along with DC reflectance of the probe laser beam. The modulated optical reflectance signal and DC reflectance are compared with reference signals generated from calibration substrates to determine carrier activation and end-of-range defect density in the junction.