The dynamic soil-structure interaction of a shear wall embedded in elastic isotropic and homogeneous soil layers underlain by bedrock, subjected to SH waves, is modeled in the present article. The soil layers consist of irregular interfaces and it has been shown that the scattering due to the roughness of the layers has significant effect on the displacement of both the foundation and the shear wall. To demonstrate the phenomena indirect boundary element method (IBEM) has been used on the basis of its validation in previous problems of similar type. The system response is compared with the analytical solution of the same type of model for vertically propagating incident SH waves. It is observed that for the low frequency of wave, displacement is abruptly high, and as a result the combination of shear wall and foundation perceives resonance. The thickness of the soil layer, mass of the shear wall, stiffness of the bedrock and the soil layers all affects the system frequency and displacement.