An original methodology is developed for scanning of the arterial intima morphology using the atomic force microscopy. The probing nanolaboratory NTEGRASpectra (NT-MDT, Russia) was itilized. The pictures of the coronary artery intima topology were obtained with the resolution of 1 nm. The 3D model of the ‘endothelial cell surface - low density lipoprotein (LDL)’ complex was constructed. Using the ANSYS software, the deformation of LDL particle was found as well as the stress distribution at the moment of the macromolecule and endothelial surface collision. The largest normal and tangential stresses are found in the area of LDL interaction with the surface. These stresses are 2.173 and 0.053 kPa, respectively. It was shown that the LDL structure is being highly strained, which leads to the molecule compression and crease. Therefore, one can conclude that at the moment of LDL entering the intercellular hiatus the macromolecule will be suffering the overall deformations and large modification of its structure.