The presented paper aims to assess the geomorphology of the Sunda Trench using the scripting cartographic techniques of Generic Mapping Tools (GMT). The GMT presents one of the technical mapping alternatives to the traditional GIS with well-defined scripting approaches for geomorphological mapping and scripting functionality which enables automatization in the geomorphological studies. In this context, modelling of the geospatial datasets is processing using machine learning approaches of GMT which presents fast and accurate modelling of the unreachable regions of the Earth, the deep-sea trenches. In this case, the study focused on the analysis of the submarine geomorphology of the selected segments of the Sunda Trench, located in the Indonesian archipelago, east Indian Ocean, by GMT scripting environment. This research effort is situated in the context of the geomorphology of the Sunda Trench. The aim is to point out which differences can be identified in the slope steepness of the cross-sectional profiles in the selected geomorphological segments of the trench in its southern and northern parts, as distinct by their geological settings and geospatial location. The actuality of the present paper is the analysis of the variations of the geomorphology in Indonesia supported by the GMT-based automated, machine-based geomorphological mapping, which plays an essential role in understanding of the Earth surface processes, supports managements of natural resources, provides information for monitoring and prognosis of natural hazards and enables to predict possible changes in geomorphological evolution of the landforms.