Several embodiments of light emitting diode packaging configurations including a substrate with a cavity are disclosed herein. A patterned wafer has a plurality of individual LED attachment sites, and an alignment wafer has a plurality of individual cavities. The patterned wafer and the alignment wafer are superimposed with the LED attachment sites corresponding generally to the cavities of the alignment wafer. At least one LED is placed in the cavities using the cavity to align the LED relative to the patterned wafer. The LED is electrically connected to contacts on the patterned wafer, and a phosphor layer is formed in the cavity to cover at least a part of the LED.