Two methods, deposition method and ideal modeling based on lattice constant, are used to prepare three modulation periods’ (1.8 nm Cu/3.6 nm Au, 2.7 nm Cu/2.7 nm Au, and 3.6 nm Cu/1.8 nm Au) thin films for nanoindentation at different temperatures. The results show that the temperature will weaken the hardness of thin films. The deposition method and the formation of coherent interface will result in a lot of defects in thin films. These defects can reduce the residual stress in the thin films which is caused by the external force. The proposed system will provide potential benefits in designing the microstructures for thin films.