Bridges play an important role in transportation of modern societies. Under severe earthquakes, a bridge may lose its functionality even though the structure itself doesn’t collapse. To precisely simulate seismic response of a bridge, 3D modeling of the total structure is needed. This paper introduces a general-purpose dynamic analysis program for bridges based on 3D modeling with highlighting modeling of pounding between girders. The paper presents theory and implementation of modeling for each component of bridges. A case study of a steel elevated bridge has also been conducted.