The main objective of this paper is to present a coarse-grained material model for the simulation of threedimensional nanostructures. The developed model is motivated by the recent progress in establishing continuum models for nanomaterials and nanostructures. As there are conceptual differences between the continuum field defined in the classical sense and the nanomaterials consisting of discrete, space-filling atoms, existing continuum measures cannot be directly applied for mapping the nanostructures due to the discreteness at small length scale. In view of the fundamental difficulties associated with the direct application of the continuum approach, we introduce a unique discrete deformation measure called spatial secant and have developed a new hyperelastic model based on this measure. We show that the spatial secant-based model is consistently linked to the underlying atomistic model and provides a geometric exact mapping in the discrete sense. In addition, we outline the corresponding computational framework using the finite element and/or meshfree method. The implementation is within the context of finite deformation. Finally we illustrate the application of the model in studying the mechanics of low-dimensional carbon nanostructures such as carbon nanotubes (CNT). By comparing with full-scale molecular mechanics simulations, we show that the proposed coarsegrained model is robust in that it accurately captures the nonlinear mechanical responses of the CNT structures.