A process for modifying surfaces of zeolites and molecular sieve membranes to decrease effective pore size for separation of materials includes atomic layer controlled vapor or liquid deposition. The atomic layer controlled deposition process steps include (i) exposing the surface to a metal atom coordinated with ligand groups having bonds that are hydrolyzable to form molecular bonded structures on the surface, which structures comprise the metal atoms coordinated with the ligand group or a modified ligand group and then (ii) hydrolyzing the bonds and possibly, but not necessarily, cross-linking the bonds in the ligand or modified ligand group.