Multibeam echo-sounders provide ideal data for semi-automated seabed feature extraction and accurate morphometric measurements. However, these methods have not been tested in morphologically highly complex environments. In this study, bathymetric and raw backscatter data were initially used to manually map the complex reef morphology found in the semi-enclosed Gera Gulf, in the northern Aegean Sea (Greece). A large number of reefs (more than 7000) were detected, making manual mapping extremely time-consuming. Benthic Terrain Modeller (BTM) was selected as a semi-automated method to map the reefs. The BTM did not function properly in this irregular relief and the results were discouraging. Trying to improve the BTM functionality, both bathymetry and slope were modified (enhanced); this time, the BTM outcome was unexpectedly improved, producing accurate results that appeared to exceed the accuracy of manual mapping. To compare the final maps with the distribution of the reefs, mapcurves were created to estimate the Goodness-of-Fit (GOF), while Precision, Recall, and F1 Score were also calculated. GOF values suggest more than 50% overlap between the resulting polygons while, Precision, Recall and F1 score resulted in values higher than 0.78 suggesting good detection accuracy for the semi-automated method. It becomes apparent that BTM provided more efficient results in comparison to the time-consuming manual mapping. This study asserts that semi-automated mapping stands as an effective method for delineating the geomorphometry of intricate relief and serves as a powerful tool for habitat mapping and decision-making.