Predicting soil behavior under dynamic load due to earthquakes is pivotal for engineering structures and human life. Due to various limitations, such as insufficient computers and difficulties in generating models, the third-dimension effect is generally neglected in many studies. Conversely, the third-dimension effect in regions with high topographic differences, deep basins, three-dimensional heterogeneous and anisotropic environments, and alluvium is at a level that cannot be neglected. This study created a three-dimensional model of the northwest of Turkey for the first time by including surface topography. Soil properties were added to this model, and dynamic analysis was performed. This new model aims to increase the accuracy of ground motion predictions in Northwest Turkey. The accuracy of this model was analyzed using real earthquake data recorded in the study area. In addition, a new software (SiteEffect3D) with various features has been developed to create a three-dimensional mesh with topography using digital elevation model data and to perform dynamic analysis more effectively. This software has been tested comparatively with “Plaxis 3D” software using synthetic terrain models. The importance of this study is that in addition to its contributions to site response analysis and seismic hazard assessment, new software has been developed that can be used in similar studies. The findings will provide valuable information for seismic design and construction practices and facilitate the development of more effective strategies to reduce the potential damage from earthquakes in the region.