A system and method for heating a substrate while that substrate is being processed by an ion beam is disclosed. The system comprises two arrays of light emitting diodes (LEDs) disposed above and below the ion beam. The LEDs may be GaN or GaP LEDs, which emit light at a wavelength which is readily absorbed by silicon, thus efficiently and quickly heating the substrate. The LED arrays may be arranged so that the ion beam passes between the two LED arrays and strikes the substrate. As the substrate is translated relative to the ion beam, the LEDs from the LED arrays provide heating to the substrate.