Substrate temperature control apparatus and electronic device manufacturing systems provide pixelated light-based heating to a substrate in a process chamber. A substrate holder in the process chamber may include a baseplate. The baseplate has a top surface that may have a plurality of cavities and a plurality of grooves connected to the cavities. Optical fibers may be received in the grooves such that each cavity has a respective optical fiber terminating therein to transfer light thereto. Some or all of the cavities may have an epoxy optical diffuser disposed therein to diffuse light provided by the optical fiber. A ceramic plate upon which a substrate may be placed may be bonded to the baseplate. A thermal spreader plate may optionally be provided between the baseplate and the ceramic plate. Methods of controlling temperature across a substrate holder in an electronic device manufacturing system are also provided, as are other aspects.