The publication is focused on the problem of nanoparticle aggregation on the sublimation interface between vacuum and rapid frozen liquid dispersion. The main aims are simulation experiments of mathematical modelling of these processes. During lyophilization of rapid frozen liquid dispersion of nanoparticles, a self-organization of nanoparticles occurs. The resulting structure depends on setting the process parameters. According to the current knowledge, they include temperature, vacuum depth, and nanoparticle fraction in the dispersion liquid. On the free sublimation interface, a streamlined flow of dispersion liquid molecules, also referred to as sublimation wind, flows into the vacuum. Lamellar nanoparticle aggregates are formed on the interface surface in this mode, which are gradually torn by the pressure of the sublimation wind. Aggregated materials with very high specific surface area may be formed by these processes. Mathematical modelling of nanoparticle dynamics on two-dimensional sublimation layer is employed to deepen the understanding of basic mechanisms of these aggregation processes. The simulation results are in good agreement with the experimental results of lamellar nanostructure aggregation of bonded globular nanoparticles nC60. Further refinements based on the simulation experiments will allow active control of the process and quality of aggregated nanostructures.