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The method of numerical modeling of heat transfer between three-dimensional objects being in contact is described in the paper. Presented approach is based on the finite element method (FEM) with independent spatial discretization of considered regions. The gap between external surfaces of the interacting objects has variable width and is filled with gas or liquid. The medium in the gap introduces thermal resistance into heat transfer process. The mathematical model of considered problem is based on the equation of heat diffusion supplemented by the appropriate initial and boundary conditions. The deformations of the regions resulting from the mechanical contact and thermally dependent changes of their volumes are also included in the model. The results of numerical simulations are presented and discussed.