Site and topography effects are integral part of strong ground motion recorded during an earthquake. Site effects due to shallow subsurface velocity and topographic changes have been clearly seen in the Gorkha earthquake, 25th April, 2015 ($M_w$ 7.8) at Kapkot and Berinag stations, which lies at an epicentral distance of 507 and 485 km, respectively. The high peak ground acceleration was recorded at Kapkot station that is at valley, while comparatively low peak ground acceleration was recorded at Berinag station that is at hill. This paper investigates the effect of site topography and shallow velocity structure on ground acceleration generated due to propagation of SH wave generated by a finite far-field rupture. The propagation of SH wave in a shallow subsurface earth model with the vertical variation of velocity can be modelled by finite difference (FD) method based on staggered algorithm that can effectively model the propagation of the seismic wave in isotropic as well as heterogeneous elastic medium. This paper discusses the role of staggered algorithm in the generation of particle motion at the surface of modelled earth characterized by surface topography and vertical distribution of elastic constants. The developed software for FD modelling of the medium has been tested for SH wave propagation in a purely elastic medium in terms of numerical stability, dispersion and boundary conditions. Numerical experiments show that the method effectively models the topography and thin surface velocity layers in the model for varying cases. The obtained surface acceleration records from the propagation of SH wave at Kapkot and Berinag clearly show that both the site amplification and topographic effects have played a vital role in shaping the accelerograms at these stations.