A 9 km wide, 92 km long, three-dimensional (3-D) seismic reflection volume acquired off Shikoku Island, Japan, images the seaward portion of the subduction of the Philippine Sea plate at the Nankai Trough and Nankai accretionary prism. Detailed interpretation of the imbricate thrust and protothrust zones, the portions of the prism between the deformation front and the first out-of-sequence thrust, shows a high degree of variability in the thrust faults that all parallel the frontal thrust but are arranged in en echelon patterns along strike and frequently include complications such as piggyback faults and fault splays. Interestingly, the sinuous seafloor morphology of the prism does not accurately reflect the en echelon 3-D architecture of the primary prism thrusts. Seafloor morphology appears to average across several thrusts along strike and is further modified by near-surface thrust splays and backthrusts, suggesting that care must be taken in interpreting seafloor relief in terms of lateral continuity or thrust fault geometry. Subduction of the Kinan seamounts 20 km northeast of the center of the Muroto 3-D volume generated a scallop-shaped embayment in the prism; the rebuilding process appears to influence the northeastern portion of the 3-D volume where a ~625 m landward step in the position of the frontal thrust and numerous changes in prism architecture are observed. These observations imply that accretionary prisms may reattain equilibrium following seamount subduction by lateral en echelon fault propagation into damaged zones that facilitate an increase accretion rate until a laterally continuous deformation front is reestablished.