The study present a case study of the Generic Mapping Tools (GMT) applied for cartographic modelling, mapping and comparative analysis of the deep-sea trenches located in southwest Pacific Ocean: the New Britain Trench (NBT) and the San Cristobal Trench (SCT). The aim was to evaluate their geomorphic variation using scripting cartographic approach of GMT. The data was processed using a sequence of the GMT modules with the main module 'grdtrack' used to visualize crosssection profiles along the trenches for their geomorphological modelling. The main grid used for topographic mapping is the SRTM DEM with 15-arc second resolution. The statistical analysis shown variability in depths of both trenches by samples in two transects. The cartographic analysis demonstrated following results. The SCT is generally deeper reaching-9,000 m, while the median for the NBT less then 7,000 m. The gradient slope of SCT is more symmetric with accurate 'V' form. In a cross-section graph, the NBT landward slope is markedly asymmetric U-shaped form and has a crescent form in the east. The NBT slope dips westwards with 35° eastward, and 41° westward, while the SCT slope has 33° oceanwards and 33,69° landwards. The difference between the geomorphology of the trenches is explained by the effects of the geotectonic evolution and actual sedimentary processes affected their formation and sculptured their structure. The marine free-air gravity anomaly illustrated density anomalies at the bathymetry in the region of NBT and SCT with range <-60.0 mGal. The geoid values are 56-66 mGal. The study contributed to the submarine geomorphic mapping and presents technical application of the cartographic functionality of GMT used for geomorphological modelling.