A detailed technique has been developed in terms of a molecular dynamics method, which allows for the detailed investigation of a wide range of phenomena occurring in crystals as a result of different thermal and mechanical influences. This method has been applied to the numerical simulation of several types of real thermo-mechanical treatment (TMT) and to the qualitative and quantitative comparison of the course of recrystallization, structure and stability of the crystals obtained. Possible reasons and methods of the loss of stability of the systems are discussed. Two model methods of stabilization were observed.