Developing new techniques for the prediction of materials behaviors in nano-scales has been an attractive and challenging area for many researches. Molecular Dynamics (MD) is the popular method that is usually used to simulate the behavior of nano-scale material. Considering high computational costs of MD, however, has made this technique inapplicable as well as inflexible in various situations. To overcome these difficulties, alternative procedures are thought. Considering its capabilities, Finite Element Analysis (FEA) seems to be the most appropriate substitute for MD simulations in most cases. But since the material properties in nano, micro, and macro scales are different, therefore to use FEA methods in nano-scale modeling one must use material properties appropriate to that scale. To this end, a previously developed Hybrid Molecular Dynamics-Finite Element (HMDFE) approach was used to investigate the nanoindentation behavior of single crystal silicon with Berkovich indenter. In this study, a FEA model was developed based on the material properties extracted from molecular dynamics simulation of uniaxial tension test on single crystal Silicon. Eventually, by comparison of FEA results with experimental data, the validity of this new technique for the prediction of nanoindentation behavior of Silicon was concluded.