In this paper we report some investigations on the problem of controlling isomerization for small polyatomic non-rigid molecules, using the LiNC/LiCN system as an example. Two methods of control in the classical ensemble of LiNC/LiCN system are described and analyzed by performing computer simulations for the corresponding canonical ensemble. The first method is based on controlling the total energy. The second one is based on changing the minimum energy path profile, and the potential energy surface for a certain "representative" configurations of the molecule. The algorithm used in both cases is based on the speed-gradient principle. The control function obtained in the classical mechanical study, with the total energy control algorithm, is subsequently applied to the quantum mechanical ensemble of LiNC/LiCN molecules. The quantum mechanical calculations are carried out within a finite basis approximation, consisting of 14 energy levels and the corresponding eigenfunctions. A comparison between the simulation results for the classical and quantum models shows a reasonable similarity in the performance on the control.