This paper presents the formulation and application of a multiscale methodology that couples three domains using a finite element framework. The proposed method efficiently models atomistic systems by decomposing the system into continuum, bridging, and atomistic domains. The atomistic and bridging domains are solved using a combined finite element–molecular mechanics simulation where the system is discretized into atom/nodal centric elements based on the atomic scale finite element method. Coupling between the atomistic domain and continuum domain is performed through the bridging cells, which contain locally formulated atoms whose displacements are mapped to the nodes of the bridging cell elements. The method implements a temperature-dependent potential for finite temperature simulations. Validation and demonstration of the methodology are provided through three case studies: displacement in a one-dimensional chain, stress around nanoscale voids, and fracture. From these studies differences between multiscale and fully atomistic simulations were very small with the simulation time of the proposed methodology being approximately a tenth of the time of the fully atomistic model. Copyright © 2012 John Wiley & Sons, Ltd.