With ever increasing the applications of metal matrix nanocomposites (MMNCs) reinforced with carbon nanofillers, demand for accurate and effective modeling techniques in this area has been increased in recent years. To provide such a route, this study is dedicated to apply information form interfacial atomic interactions in modified continuum models implemented to analyze the mechanical behavior of these nanocomposites. In the proposed methodology, the metal matrix is considered as a continuous medium. Meanwhile, to capture the atomicscale phenomena governing the problem, the carbon nanofiller, local metal atoms neighboring it, and the nanofiller/metal interface are analyzed using molecular dynamics (MD) simulations. Subsequently, employing the equivalent continuum modeling (ECM) concept, geometrical and mechanical characteristics of the equivalent nanofiller is obtained in each case and introduced in a finite element analysis (FEA). It is demonstrated that the atomistically informed FEA can successfully reproduce the results of full atomistic MD simulations with ignorable run-time compared to that of this method. Finally, constructing several computational cells with different metal matrices and reinforcing agents, the developed MD/FE multiscale approach is utilized to capture the influences of temperature, nanofiller geometry and orientation, its volume fraction and interfacial interactions on the axial elastic constants of these nanocomposites.