The development of heterostructures based on two-dimensional (2D) materials such as graphene, hexagonal boron nitride (h-BN), and transition metal dichalcogenides (TMD) has become a central focus in modern materials science [1]. Of special interest are hybrid organic/inorganic heterostructures, which are able to perform precise tuning of physical and chemical properties at the molecular level due to fabrication. By combining the structural precision of 2D inorganic layers with the chemical versatility of organic components, these systems allow for the design of atomically sharp interfaces, paving the way for advanced (opto)electronic devices with tailored functionalities and enhanced performance. Here, we investigate monomolecular layer clusterization based on F4TCNQ molecules formed on two-dimensional materials: graphene, hexagonal boron nitride, MoS2 and their heterostructure [2]. The local ordering of molecules in monomolecular layer is an important characteristic to predict their electronic properties through the interaction between organic molecules and the underlying substrates. By means of state-of-the-art computational methods including DFT, molecular dynamics and machine learning we show the influence of point and line defects on the local ordering of F4TCNQ molecules and physical and chemical properties and step-by-step formation process. The work was supported by the Russian Science Foundation (No. 25-73-10250, https://rscf.ru/project/25-73-10250/). [1] A. K. Geim, I. V. Grigorieva, Nature 2013, 499, 419. [2] D. G. Kvashnin, V. S. Baidyshev, FlatChem 2023, 42, 100585.