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In this paper, an advanced formulation of the spectral finite element method (SFEM) is presented and applied in order to carry out site response analysis of 2D topographic structures subjected to vertically propagating incident in-plane waves in time-domain. The accuracy, efficiency and applicability of the formulation are demonstrated by solving some wave scattering examples. A numerical parametric study has been carried out to study the seismic response of rectangular alluvial valleys subjected to vertically propagating incident SV waves. It is shown that the amplification pattern of the valley and its frequency characteristics depend strongly on its shape ratio. The natural frequency of the rectangular alluvial valley decreases as the shape ratio of the valley decreases. The maximum amplification ratio along the ground surface occurs at the center of the valley. A simple formula has been proposed for making initial estimation of the natural period of the valley in site effect microzonation studies.