In this work we propose two ways of tuning of the optical properties of a fishnet metamaterial infiltrated by liquid crystal. The first method is to control the hole mode of the structure via the reorientation of the liquid crystal molecules. We show that in this case the system is mainly sensitive to the refractive index change occurring inside the holes. The second technique is to tune surface-plasmon polariton modes. In this instance the structure becomes sensitive mainly to the refractive index change at the metal-liquid crystal interface. We demonstrate that controlling the surface modes one can achieve higher variation of the effective index (more than 300 times index enhancement), however transmission in such a system is lower than for the case of the hole mode control.