The endokarst landscape is the result of long erosion and sedimentation processes that have modelled an environment in which capricious forms abound. Despite being a hostile environment for human life, these caves must have attracted the attention of human groups from as early as the Palaeolithic. It is striking that many examples of rock art appear to be closely symbiotic with their natural support; nevertheless, it is difficult to confirm any relationship in the distribution of the decorated spaces, based on their morphology. Moreover, if we start from the hypothesis—widely accepted, but not demonstrated—that Palaeolithic cave art is a system of visual communication, the visibility of the art or the number of people who could be accommodated in the decorated sectors should be determining factors. In order to avoid making subjective appraisals when analysing these factors, we have designed a Python script with a workflow to work directly with 3D models of caverns using GISs, which can be easily replicated and edited by other researchers. Application of this script in the Magdalenian caves of Atxurra, Santimamiñe and Altxerri (Northern Spain) has allowed us to compare them accurately based on their visibility features. This has shown that in some cases, there may have been prior planning to enhance the visibility of some figures. In all cases, the groups of figures are located in deep and hidden parts of the caves, usually in sectors with limited capacity to accommodate people, which would be consistent with a system of restricted communication.