When assessing seismic risk at a city scale, local site conditions can significantly modify the destructive potential of an earthquake. This was the case in Mexico City in 1985 and 2017, which is located on a sedimentary valley. For that reason, characterization and consideration of these site effects, in addition to assessing the probability of occurrence of a destructive earthquake in a given region, are crucial. For this purpose, a tri-dimensional model was developed using a numerical code that permit to carry out such kind of studies. The code is based on the spectral element method allowing solving the waves propagation problem in tri-dimensional solid media. The seismic phenomenon is simulated in its entirety: from the seismic source to the site using a representative model of the complexity of the wave path. However, this introduces uncertainties that must be quantified, controlled and reduced by validating the results of the numerical tool with measurements on a real study site. This work aims to study numerically the effect of the geometric structure of soil and subsoil on the prediction of ground motion at the regional scale. The first obtained results show the importance of the in-situ measures on the regional scale simulations.