This study proposes a novel methodological approach to reconstructing the boundaries and structure of medieval settlements without relief features. In recent centuries, the areas of most sites were used for plowing, destroying their relief features. Erosion eventually redistributed the soil of the destroyed occupation layers. Therefore, not only the area of a site must be studied, but the adjoining areas as well. Tendencies in the distribution of the transported occupation layer mirror the thickness of the original culture-bearing deposits. Such estimates can be obtained by collating archaeological and science-based data. First, multispectral aerial photographs are subjected to statistical analysis. The results are then used to subdivide the settlement territory into smaller areas differing in vegetation density. Comparison with the results of geophysical, soil, and archaeological studies allows us to interpret those areas, to assess the state of preservation of the occupation layer (superficially disrupted, replaced, or transported). Previous multidisciplinary studies at the Kushman cluster of sites (9th–13th centuries AD) revealed substantial differences from the traditional classification (fortified settlement and group of unfortified rural settlements). Two sites can be defined as fortified settlements (Uchkakar and Kushmanskoye III), whereas Kushmanskoye II is an economic development area. The use of statistical analysis of multispectral imaging enabled us not only to confirm the previously proposed reconstruction, but also to substantiate the hypothesis about the initial boundaries and structure of the settlements.