Damage detection of existing structures is one of the important topics in term of maintenance and retrofitting. Seismic tomography is one of the methods of identification and has been applied for various field of engineering that includes damage detection of existing structures. This is typically conducted on two dimensional models; however, three-dimensional tomography is required due to the consideration of three dimensional extent of damage area. This paper presents a three dimensional identification algorithm that is represented by combination of the ray-trace algorithm and SIRT (Simultaneous Iterative Reconstruction Technique) for the three-dimensional seismic tomography for existing structures. The ray-trace algorithm is based on Huygens's principal and the space for the ray-trace is subdivided into hexahedron elements. The shape of each element is described by first-order isoparametric element that is commonly used by finite element analysis. This feature enables that the mesh data for ray-trace can be prepared by pre-processor for finite element analysis. The presented method is applied for an existing structure to check the feature and applicability of the presented method.