There is disclosed herein a method of making a device made up of at least two separate parts each of which is formed of a patterned array with the parts being mounted one on the other, with the patterned arrays of the parts being aligned, such as a CCD imager having a color filter thereon. The two parts are made on separate substrates with a first alignment key being formed on each substrate. The first alignment keys are formed by photolithography using the same mask to form the first alignment keys on each substrate. The various features of each of the parts are then formed on each substrate with each feature being formed by a photolithographic step using a mask which is aligned to a first alignment key so as to align all the features. A second alignment key is formed on each substrate and is positioned on each substrate in the same relationship with a first alignment key. The second alignment keys are of a material and construction so as to be visible when radiation of a desired wavelength is directed through the substrates. A part formed on one of the substrates is placed over a part formed on the other substrate. Radiation is directed through the substrates and the second alignment keys are aligned so as to align the patterned array of the two parts
