Emitter packages are disclosed having a thixotropic agent or material, with the encapsulant exhibiting significant reduction of thixotropic agent scattering. The packages exhibit a corresponding reduction or elimination of encapsulant clouding and increased package emission efficiency. This allows for the thixotropic agents to be included in the encapsulant to alter certain properties (e.g. mechanical or thermal) while not significantly altering the optical properties of the encapsulant. One embodiment of a light emitting diode (LED) package according to the present invention comprises an LED chip with an encapsulant over the LED chip. The encapsulant has an encapsulant refractive index and also has a thixotropic material with a refractive index that is substantially the same as the encapsulant refractive index.