Nanoimprinting lithography is considered to be one of the methods with the most potential for the fabrication of nano-structures. This study proposes an alternative manufacturing process, the direct imprint method, which is different from nanoimprinting lithography and which is employed in the fabrication of metallic thin-film nano-structure. A three-dimension molecular dynamics simulation is utilized to simulate the imprinting process. The effects of the thin-film thickness and the line width of the mold on the formation of metallic patterns are also investigated. In the molecular dynamics simulation model, the metallic thin film and the mold, made of gold and nickel, respectively, are formed in face central cubical single crystal. The simulation results show that during the imprinting process, by varying the thickness of thin films and the line width of the mold, the mechanical properties such as hardness and stress will change and have a great effect on the formation of metallic patterns. The substrate effect appears during the imprinting process, and that is an important factor in the manufacturing process. Following the simulation, an experimental investigation is performed as comparison. This includes two experiments, nanoindentation and direct nanoimprinting. The former characterizes the mechanical properties of thin films on the substrate while the latter illustrates the formation of metallic patterns. It has been found that the effects of thin-film thickness on the formation of metallic patterns correspond very well both in simulation and experimental results.