A recently proposed three-dimensional (3D) linear method for examining soil-building interactions based on an input seismic wave field is, after some improvements, applied to estimate seismic building responses in the reclaimed zone of Tokyo Bay, where ground motions include a considerable amount of surface waves, thus reconfirming the effects of the method in a different situation. A seismic wave field involves seismic waves propagating in a 3D medium. The proposed method was developed with the goal of adequately treating seismic surface waves trapped by a (several-kilometers) deep underground structure in a soil-building interaction system. Two simulations were carried out. The first simulation successfully reproduced surface, downhole, and building accelerograms that were recorded at one borehole station during two medium-sized earthquakes. In the second simulation, seismic responses of a midrise RC model building and a wood model building were favorably calculated at the other borehole station for the 1923 Kanto earthquake. The building responses also were compared with those calculated by two standard response analyses, demonstrating the superiority of the proposed method.