Voronoi diagram and Delaunay tessellation have been used for a long time for structural analysis of computer simulation of simple liquids and glasses. However the method needs a generalization to be applicable to molecular and biological systems. Crucial points of implementation of the method for analysis of intermolecular voids in 3D are discussed in this paper. The main geometrical constructions - the Voronoi S-network and Delaunay S-simplexes, are discussed. The Voronoi network "lies" in the empty spaces between molecules and represents a "navigation map" for intermolecular voids. The Delaunay S-simplexes determine the simplest interatomic cavities and serve as building blocks for composing complex voids. An algorithm for the Voronoi S-network calculation is illustrated on example of lipid bilayer model.