In one embodiment, the transparent growth substrate (38) of an LED die is formed to have light scattering areas (40A-C), such as voids formed by a laser. In another embodiment, the growth substrate is removed and replaced by another substrate that is formed with light scattering areas. In one embodiment, the light scattering areas are formed over the light absorbing areas of the LED die, to reduce the amount of incident light on those absorbing areas, and over the sides (42A, 42B) of the substrate to reduce light guiding. Another embodiment comprises a replacement substrate may be formed to include reflective particles in selected areas where there are no corresponding light generating areas in the LED semiconductor layers such as -type metal contacts (28). This prevents reabsorption into absorbing regions of the semiconductor layer thereby enhancing external efficiency of the device. A 3D structure may be formed by stacking substrate layers containing the reflective areas. The substrate may be a transparent substrate or a phosphor tile (20) that is affixed to the top of the LED.