The results of the scientific research presented in this paper are focused on solving an important scientific and technical problem – enhancing the efficiency of the grain material separation process using a vibro-pneumatic method with the application of mechanical intensifiers to obtain high-quality seed material. The relevance of the study is substantiated, and the key factors influencing the increase in productivity and the improvement of quality in seed material preparation processes are analyzed. A critical review of the existing literature related to the research topic is conducted, and promising approaches for addressing the identified challenges are determined. The paper presents mechanical and mathematical models of the separation process of seed materials based on seed density on working surfaces equipped with mechanical intensifiers. In developing multidimensional mathematical models of the separation process, it is assumed that under the combined action of a directed airflow and oscillations of the working surface, effective vertical stratification of the pseudo-fluidized seed material occurs. As a result, N layers of particles are formed, each characterized by their own density, aerogravitational, and hydrodynamic properties. The motion of each particle layer is considered within the framework of multiphase continuum mechanics, where each layer is modeled as a separate continuous medium, and the interactions between layers are described through boundary conditions at their interfaces. Thus, the dynamics of the vertically stratified pseudo-fluidized particle bed can be described as the motion of an (N + 1)-phase system consisting of N layers of discrete particles and one continuous gas phase (air). When modeling particle density, it is assumed that limiting density values exist for the “light” fraction (including difficult-to-separate impurities, damaged and substandard seeds with reduced density) and the “heavy” fraction (biologically viable and active seeds with higher density). Between these limiting values lies the “medium” fraction, which contains particles with intermediate density characteristics.