We use molecular simulations to analyze the preferential adsorption sites of molecules that differ in size, shape, and polarizability in Cu-BTC metal organic framework. The cage system of the framework can be exploited to enhance adsorption of small gases. We find that nonpolar molecules adsorb preferentially in the small tetrahedral cages, whereas alcohols and water molecules adsorb close to the copper atoms in one of the big cages. Blocking potentially enhances selective adsorption and separation and we therefore investigate how to block these cages in a practical manner. We propose to use ionic liquids for it and we find that the addition of these components reduces the adsorption of polar molecules near the open metal centers. For this reason, the presence of ionic liquids reduces the attack of the molecules of water to the metallic centers improving the framework stability.