A method for aligning a plurality of sub-apertures of a multiple-aperture imaging system including, but not limited to, identifying one sub-aperture to serve as a reference sub-aperture, actuating the reference sub-aperture in a series of piston steps of a known amount, collecting data relating to each image of a plurality of images of a point object, each image corresponding to a respective piston step, compiling the data into a three-dimensional data cube, detecting a plurality of fringes positioned within the three-dimensional data cube, determining the relative location of each sub-aperture of the plurality of sub-apertures based on a location of each fringe of the plurality of fringes within the three-dimensional data cube, and actuating a piston associated with at least one sub-aperture based, at least in part, on the relative location to move the at least one sub-aperture into alignment with another sub-aperture and repeating with each remaining sub-aperture until all sub-apertures are at substantially the same piston height.