1. A method for actively aligning a lens stack array with a sensor that includes a plurality of focal planes, where each focal plane comprises a plurality of rows of pixels that also form a plurality of columns of pixels and each focal plane is contained within a region of the imager array that does not contain pixels from another focal plane, the method comprising: aligning the lens stack array relative to the sensor in an initial position, where the lens stack array comprises a plurality of lens stacks and the plurality of lens stacks forms separate optical channels for each focal plane in the sensor; varying the spatial relationship between the lens stack array and the sensor; wherein varying the spatial relationship comprises one of tipping, tilting, or rotating the lens stack array relative to the sensor; capturing images of a known target using a plurality of active focal planes at different spatial relationships between the lens stack array and the sensor, where the known target includes at least one region of interest; scoring the images captured by the plurality of active focal planes, where the resulting scores provide a direct comparison of the extent to which at least one region of interest is focused in the images; selecting a spatial relationship between the lens stack array and the sensor based upon a comparison of the scores of images captured by a plurality of the active focal planes; and forming an array camera subassembly in which the lens stack array and the sensor are fixed in the selected spatial relationship.