Three-dimensional geometrically and physically nonlinear problems of nonstationary deformation of structures are considered. The defining system of equations is formulated in Lagrange variables. The equation of motion is derived from the balance of virtual work capacities. The elastic-plastic deformation of structural materials is described by the relations of the flow theory with isotropic hardening. The solution of the problem is based on the moment scheme of the finite element method. The discretization of the problem by spatial variables is carried out by eight nodal finite elements with multilinear functions of the approximation form of the displacement velocity. Time integration is performed according to an explicit finite-difference scheme of the “cross” type, which does not have the monotonicity property. Due to the dispersion in the vicinity of the gap, it generates non-physical oscillations, which significantly limits the scope of its applicability. In this paper, to suppress high-frequency oscillations, it is proposed to use an algorithm for conservative smoothing of a numerical solution with a space-time monotony analyzer. Based on it, software modules have been developed for the “Dynamics-3” computing complex. Verification of the developed technique and its software implementation was carried out by solving a one-dimensional problem in a three-dimensional formulation of the compression wave passing through a fixed elastic layer. For comparison, the results of numerical solution of the problem according to the “cross” scheme without smoothing, with linear viscosity, with conservative smoothing using spatial and spatiotemporal monotonicity analyzers are obtained. The problem of penetration of an elastic cylinder into a round steel plate is solved in a three-dimensional formulation. It is shown that the developed technique not only suppresses high-frequency oscillations, but also prevents the occurrence of zero-energy modes. So, in the second problem, without using the procedure of conservative smoothing of the numerical solution, the final elements of the plate in the collision zone are significantly distorted, which leads to an early interruption of the calculation.