The modern theory of cultural layer is based on idea of indissoluble links of processes of formation and destruction of a layer of the cultural remains. The cultural remains could accumulate both in the sub-aerial and in the sub-aquatic environments. Horizons in the sub-aerial deposits are the most diverse. The equally important features, that demonstrate the current state of cultural layers, depended on scenarios of destruction of the cultural remains horizons. Processes of syngenetic and epigenetic (post-genetic) deformation proceeded differently; syngenetic destruction has been substantially connected with anthropogenic influence unlike the subsequent natural processes of destruction of a layer. The most of cultural layers of the Stone Age sites, which are located in the south of East European Plain, are the result of soil and loessial deposits. A standard epigenetic deformation of horizons was determined by cryogenic and biogenic processes and moved up and down of objects in a burial cultural layer. The degree of such deformation ranged from moderate to highly significant. The method of linking the details of the flint applications makes it possible to confidently diagnose the original stratigraphic position of the cultural layer and, in some cases, reconstruct the topography of a surface of habitation. Weak destruction of sections of the cultural layer with a dense (pressed) mass of cultural remains is noted.