Methods for processing semiconductor materials and substrates with a focused or collimated light beam. Light may be directed on a sample to alter material properties at a depth below the surface. The focused light beam has a peak power density positioned at a selected depth, and absorption of light energy, resulting from selection of wavelength and optical characteristics of the substrate as a function of depth, results in process effects taking place over a preferred limited range of depth. For example, process effects such as curing, annealing, implant activation, selective melting, deposition and chemical reaction may be achieved at dimensions limited by the light beam density in the vicinity of the focused beam spot. The wavelength may be selected to be appropriate for the process effect chosen. The beam may be scanned over the substrate to selectively provide processing effects.