Topographic conditions play an important role on the modification of seismic ground motion. Therefore, their effects may become crucial in the selection or simulation of ground motion for use in structural seismic response analysis. In this research, topography effects of canyon sites are analyzed using a three-dimensional boundary element procedure. The multi-domain boundary element method proposed by Ahmad and Banerjee is used for three-dimensional cases with good accuracy. Effects of model parameters (free-field and canyon lengths) are well accounted for ensuring accurate results. It is shown that the free-field (both side of the canyon cross-section) length is less influential than the canyon length. Some general rules for the three-dimensional boundary element modeling of wave scattering problem are proposed. In addition, effects of different wave parameters (frequency and direction), material properties (damping ratio and poisson's ratio) and canyon geometry are investigated. It is demonstrated that the effect of canyon shape and canyon depth on the topographic amplification is frequency dependent. Deep canyon (semi-circular canyon) induces larger amplification effect than shallow canyon (semi-elliptical canyon) in different frequencies.