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Despite the recognized effectiveness of LiDAR in penetrating forest canopies, its capability for archaeological prospection can be strongly limited in areas covered by dense vegetation for the detection of subtle remains scattered over morphologically complex areas. In these cases, an important contribution to improve the identification of topographic variations of archaeological interest is provided by LiDAR-derived models (LDMs) based on relief visualization techniques. In this paper, diverse LDMs were applied to the medieval site of Torre Cisterna to the north of Melfi (Southern Italy), selected for this study because it is located on a hilly area with complex topography and thick vegetation cover. These conditions are common in several places of the Apennines in Southern Italy and prevented investigations during the 20th century. Diverse LDMs were used to obtain maximum information and to compare the performance of both subjective (through visual inspections) and objective (through their automatic classification) methods. To improve the discrimination/extraction capability of archaeological micro-relief, noise filtering was applied to Digital Terrain Model (DTM) before obtaining the LDMs. The automatic procedure allowed us to extract the most significant and typical features of a fortified settlement, such as the city walls and a tower castle. Other small, subtle features attributable to possible buried buildings of a habitation area have been identified by visual inspection of LDMs. Field surveys and in-situ inspections were carried out to verify the archaeological points of interest, microtopographical features, and landforms observed from the DTM-derived models, most of them automatically extracted. As a whole, the investigations allowed (i) the rediscovery of a fortified settlement from the 11th century and (ii) the detection of an unknown urban area abandoned in the Middle Ages.