The article addresses the issue of clustering of multidimensional data arrays with a noise using the methods of discrete mathematical analysis (DMA clustering). The theory of DMA clustering through the logical densities calculus is detailed, and the new algorithm Linear Discrete Perfect Sets (LDPS) is described. The main objective of the LDPS algorithm is to identify linearly stretched anomalies in a multidimensional array of geo-spatial data (geophysical fields, geochemistry, satellite images, local topography, maps of recent crustal movements, seismic monitoring data, etc.). These types of anomalies are associated with tectonic structures in the upper part of the Earth’s crust and pose the biggest threat for integrity of the isolation properties of the geological environment, including in regions of high-level radioactive waste disposal. The main advantage of the LDPS algorithm as compared to other cluster analysis algorithms that may be used in arrays with a noise is that it is more focused on searching for clusters that are linear. The LDPS algorithm can apply not only in the analysis of spatial natural objects and fields but also to elongated lineament structures.