We propose a complete superradiant and subradiant states that can be manipulated and prepared in a three-dimensional atomic array. These subradiant states can be realized by absorbing a single photon and imprinting the spatially-dependent phases on the atomic system. We find that the collective decay rates and associated cooperative Lamb shifts are highly dependent on the phases we manage to imprint, and the subradiant state of long lifetime can be found for various lattice spacings and atom numbers. We also investigate both optically thin and thick atomic arrays, which can serve for systematic studies of super- and sub-radiance. Our proposal offers an alternative scheme for quantum memory of light in a three-dimensional array of two-level atoms, which is applicable and potentially advantageous in quantum information processing.