A method for controlling the thermal boundary conditions of non-equilibrium molecular dynamics simulations by concurrent coupling with a continuum far field region is presented. The method is simple to implement into a conventional molecular dynamics code and independent of the atomistic model employed. It regulates the temperature in a thermostatted boundary region by feedback control to achieve the desired temperature at the edge of an inner region where the true atomistic dynamics are retained. This is necessary to avoid intrinsic boundary effects in non-equilibrium molecular dynamics simulations. A stadium damping thermostat is employed to avoid the adverse reflection of phonons that occurs at an MD interface. The effectiveness of the algorithm is demonstrated for the example of transient heat flow down a three-dimensional atomistic composite rod.