Multi-beam, multi-wavelength processing systems include two or more lasers configured to provide respective beams to a substrate. The beams have wavelengths, pulse durations, beam areas, beam intensities, pulse energies, polarizations, repetition rates, and other beam properties that are independently selectable. Substrate distortion in processes requiring local heating can be reduced by preheating with a large area beam at a first wavelength followed by exposure to a focused beam at a second wavelength so as to heat a local area to a desired process temperature. For some processing, multiple wavelengths are selected to obtain a desired energy deposition within a substrate.