Finite element model (FEM) was used for the study and description of the arising 3D nanofiber structure strain caused by the pressure of the flowing gas. Computer simulation using an adaptive networking through implicit FEM algorithm can be utilized for a significant improvement of the study of anisotropic strain in the deformed 3D nanostructure. The created model is based on the empirical Laplace-Poisson differential equation for the flow, where gas particles are moving with certain kinetic energy. The kinetic energy depends on the speed, time and temperature and affects the resulting strain of 3D nanofiber structure. The simulation results were compared to the results obtained from the image analysis of real samples and showed that this FEM model can determine individual phases of structure strain. The comparison shows that the developed FEM model can be an important tool in the study of the strain in the arising 3D nano- fiber structure and it can provide valuable information for optimization of 3D nanofiber structure production by the electrospinning process.