In the Nankai Trough off Kii Peninsula, the first scientific drilling by D/V Chikyu commenced in September 2007 as a major component of the Integrated Ocean Drilling Program (IODP), which has been an international collaborative scientific drilling program together with 22 countries since October 2003. One of its scientific challenges is to drill through the seismogenic zone to reveal the nature and mechanism of large earthquake generation. Prior to drilling, we carried out a 2D seismic survey in 2003 to identify hazards for safe and smooth drilling operation and to obtain detailed characteristics of the accretionary prism. The 2D seismic profiles, however, have some technical limitation of imaging at some targets due to the complexities of sea floor topography and sub bottom geological structures. To extend the 2D seismic results, a high resolution 3D seismic survey was conducted by M/V Nordic Explorer (PGS) in 2006. The survey area was outside shipping lanes, and fishing activities were well managed. There was, however, a strong Kuroshio Current in the southern part of the 3D survey area which significantly affected both data acquisition and data processing. The appropriate data processing including Pre-Stack Time Migration (PSTM) was carried out by CGGAP (currently CGGVeritas). To deal with the data characteristics, the processing emphasized the following three points: swell noise attenuation, multiple reflection attenuation, and handling of irregular acquisition geometry. The seismic cube, obtained as the data processing result, shows clear images of the shallow geology and most deeper targets. The Kumano-nada 3D seismic data provided information required for the scientific drilling by D/V Chikyu, and has been providing valuable information for marine science in the area.