In the present work, a three-dimensional molecular dynamics simulation is carried out to perform the nanoindentation experiment on Ni single crystal. The substrate indenter system is modeled using hybrid interatomic potentials including the many-body potential embedded atom method (EAM), and two-body morse potential. To simulate the indentation process, a spherical indenter (diameter = 80 Å, 1 Å=0.1 nm) is chosen. The results show that the mechanical behaviour of a monolithic Ni is not affected by crystalline orientation. To elucidate the effect of a heterogeneous interface, three bilayer interface systems are constructed, namely Ni(100)/Cu(111), Ni(110)/Cu(111), and Ni(111)/Cu(111). The simulations along these systems clearly describe that mechanical behaviour directly depends on the lattice mismatch. The interface with the smaller mismatch between the specified crystal planes is proved to be harder and vice versa. To describe the relationship between film thickness and interface effect, we choose various values of film thickness ranging from 20 Å to 50 Å to perform the nanoindentation experiment. It is observed that the interface is significant only for the relatively small thickness of film and the separation between interface and the indenter tip. It is shown that with the increase in film thickness, the mechanical behaviour of the film shifts more toward that of monolithic material.