This paper represents the geometric analysis of molecular surfaces of the molecules, indicates the blending operation of an atoms constitute to the small molecules. The decision which indicates advantages of Euclidean Voronoi diagram of an atom includes the blending surface among the atoms to make a fundamental study of docking, interactions with macromolecules. The algorithm which proposes the topological part of surfaces discussed through the Euclidean Voronoi Diagram of various accessibility procedures.

Keywords: Euclidean Matrix, Voronoi Diagram, Molecular Surfaces, Non-Rigid Molecules, Melamine