Computer simulations of quantum relaxation of manganese doped A³As and A²B⁴As₂ arsenide systems have been developed. Thermodynamic conditions of these semiconductor systems stability of structural homogeneity have been investigated by the methods of molecular mechanics taking into consideration the entropic factor at various temperatures. Concentration limits of doping element providing stability of preset nanostructure of semiconductor compounds for manganese doped A³As and A²B⁴As₂ systems have been obtained. It has been shown that structurally homogeneous states of manganese doped semiconductor nanolayers has no thermodynamic stability at T = 0 K for all studied compounds and at any concentrations of alloying element. For all studied physicochemical magnetic semiconductors relaxation conditions stability of structurally homogeneous low-manganese-alloyed nanolayers increases with the temperature rise and the decrease of concentration inhomogeneity of manganese atoms distribution regardless of their concentration. With rising temperature the conversion from nanosystems with homogeneous to the inhomogeneous manganese concentration ones for structurally inhomogeneous A³As : Mn and A²B⁴As₂ : Mn nanolayers shifts to the domain of high manganese concentration.