Multiple colors of light emitted by an assembled light emitting diode (LED) based illumination device is automatically tuned to within a predefined tolerance of multiple target color points by modifying portions of wavelength converting materials associated with each color. A first color of light emitted from the assembled LED based illumination device in response to a first current is measured and a second color of light emitted from the assembled LED based illumination device in response to a second current is measured. A material modification plan to modify wavelength converting materials is determined based at least in part on the measured colors of light and desired colors of light to be emitted. The wavelength converting materials may be selectively modified in accordance with the material modification plan so that the assembled LED based illumination device emits colors of light that are within a predetermined tolerance of target color points.