Mapping seafloor geomorphology is a complex task requiring the integration of advanced cartographic technologies and high-resolution spatial data. This paper provides a comparative geomorphological analysis of the Hellenic Trench (HT) and the Pliny Trench (PT) located in the Eastern Mediterranean Sea, southern Greece. These trenches were formed as a result of the tectonic plate subduction in the Eastern Mediterranean Sea: the northward motion of the African and Ara- bian plates, complicated by the regional geological settings, such as active faults and earthquakes, which resulted in their different geomorphological forms and bathymetric shapes. Technically, this paper presents an example of the advanced scripting mapping by scripting the cartographic toolset of Generic Mapping Tools (GMT), which performs mapping through shell scripts. The maps are based on the high-quality topographic, geological and geophysical data: GEBCO, EGM96, geoid, and marine free-air gravity fields. The GMT builds upon the modules used for data processing. The region was subsetted by ‘grdcut’, analysed by the Geospatial Data Abstraction Library (GDAL) (gdalinfo utility), and visualized by ‘grdimage’. Two segments of the trenches formed in a condition of varying geological and geophysical settings, have been modelled, visualized and compared, as representative cross-sections. As a result of the automated digitizing, spatial interpolation and sequential aggregating of GMT codes, the segments of the cross-sections were represented. The HT (Ionian segment) has an asymmetric one-sided shape; a steepness of 56.8° on the NE side and 7° on the SW flank. The PT has a more symmetric view; a steepness of 42.14° on its NW flank and 26.66° on its SE flank. The PT has a clear peak of the depths at -2600 to -2800 m and the most representative data range at -5000 to -6000 m. The HT has a bimodal data distribution with two peaks. The most frequent data for HT is -3200 m to -3400 m. Compared to PT, the HT is deeper. The histogram shows the peak of data for HT in the interval between -3200 to -3400 m (135 samples) while the PT shows the peak of data in the interval at -2600 to -2800 m (310 samples). Besides, 105 samples of the HT have depths exceeding 4000 m, while only 20 samples were recorded for PT in the same interval. This paper contributes to the geomorphologi- cal studies of the general Eastern Mediterranean Sea region, particularly relating to regional seafloor mapping of the Hellenic and Pliny trenches.