This article analyzes topographical and geological settings in the Japan Archipelago for comparative raster data processing using GRASS GIS. Data include bathymetric and geological grids in NetCDF format: GEBCO, EMAG2, GlobSed, marine free-air gravity anomaly and EGM96. Data were imported to GRASS by gdalwarp utility of GDAL and projected via PROJ library. Methodology includes data processing (projecting and import), mapping and spatial analysis. Visualization was done by shell scripting using a sequence of GRASS modules: ‘d.shade’ for relief mapping, ‘r.slope.aspect’; for modelling based on DEM, ‘r.contour’ for plotting isolines, ‘r.mapcalc’ for classification, ‘r.category’ for associating labels, and auxiliary modules (d.vect, d.rast, d.grid, d.legend). The results of the geophysical visualization show that marine free-air gravitational anomalies vary in the Sea of Japan (–30 to above 40 mGal) reflecting density inhomogeneities of the tectonic structure, and correlating with the geological structure of the seafloor. Dominating values of geoid model are 30–45 m reflecting West Pacific rise, determined by deep density inhomogeneities associated with the mantle convention. Sediment thickness varies across the sea reflecting its geological development with density of 2 km in its deepest part and thinner in central part (Yamato Rise). The aspect map and reclassified map express gradient of the steepest descent.