Heritage structures are the backbone of any civilization. In a country with a rich history, the presence of heritage monuments acts as a bridge between past and present generations. Many heritage structures are vulnerable to natural and man-made calamities due to their lack of adequate seismic resistance. In order to assess the vulnerability of such structures during calamities, proper analysis and ways to retrofit them without harming their cultural and esthetic value are of prime importance. In this study, the dynamic analysis of two heritage structures in Surat, Gujarat, is carried out using 3D finite element analysis by modeling the structure and soil. The 3D model of the heritage structures is developed using image analysis to account for the complex geometries of the structures. The reconnaissance study was carried out to examine the existing damage to the historical structures and site conditions. The 3D FEM analysis was performed using Plaxis 3D using the appropriate structure properties and site conditions and considering the time history compatible with the site location. The PGA across the structure is obtained, and amplifications are evaluated for both heritage structures. It can be inferred from the amplifications observed for the two heritage structures that soil-structure interaction has a significant impact on ground response.