Zeolites are nano-porous crystals that contain channels comparable in size to molecues, and are used commercially to separate normal from branched paraffins, and to catalyze preferentially p-xylenes instead of o- and m-xylenes. The traditional method to select an appropriate zeolite to separate a set of molecules is one-dimensional screening, based on molecular and zeolite window diameters. This method is not accurate as molecules are not spheres, and molecules larger than windows can squeeze by, especially at high temperatures. An improved method is introduced here based on the two-dimensional screening of both major and minor diameters of the molecular footprints, compared to the windows. This method does not address the numerous non-elliptical windows, such as the CLO with four-leave clover shaped windows. A more advanced method is introduced here, based on the flexibilities of both the molecule and the window, by computing the minimum activation energy required to squeeze a molecule to fit a window, after suitable rotation and translation to the optimal conformation. The compilation of a database of 38 molecules and 220 zeolites makes possible the rational design of novel separation schemes.