We propose a method for efficiently coupling the finite element method with atomistic simulations, while using molecular dynamics or kinetic Monte Carlo techniques. Our method can dynamically build an optimized unstructured mesh that follows the geometry defined by atomistic data. On this mesh, different multiphysics problems can be solved to obtain distributions of physical quantities of interest, which can be fed back to the atomistic system. The simulation flow is optimized to maximize computational efficiency while maintaining good accuracy. This is achieved by providing the modules for a) optimization of the density of the generated mesh according to requirements of a specific geometry and b) efficient extension of the finite element domain without a need to extend the atomistic one. Our method is organized as an open-source C++ code. In the current implementation, an efficient Laplace equation solver for calculation of electric field distribution near rough atomistic surface demonstrates the capability of the suggested approach.