In this paper, a coupling scheme for applying finite element analysis(FEA) programs, such as, LS-DYNA and MIDAS/Civil, to a nonlinear soil structure interaction analysis by the boundary reaction method(BRM) is presented. With the FEA programs, the structure and soil media are discretized by linear or nonlinear finite elements. To absorb the outgoing elastic waves to unbounded soil region as much as possible, the PML elements and viscous-spring elements are used at the outer FE boundary, in the LS-DYNA model and in MIDAS/Civil model, respectively. It is also assumed that all the nonlinear elements in the problem are limited to structural region. In this study, the boundary reaction forces for the use in the BRM are calculated using the KIESSI-3D program by solving soil-foundation interaction problem subjected to incident seismic waves. The effectiveness of the proposed approach is demonstrated with a linear SSI seismic analysis problem by comparing the BRM solution with the conventional SSI solution. Numerical comparison indicates that the BRM can effectively be applied to a nonlinear soil-structure analysis if motions at the foundation obtained by the BRM for a linear SSI problem excluding the nonlinear structure is conservative.