Most diagrams, particularly those used in software engineering, are line drawings consisting of nodes drawn as rectangles or circles, and edges drawn as lines linking them. In the present paper we review some of the literature on human perception to develop guidelines for effective diagram drawing. Particular attention is paid to structural object recognition theory. According to this theory as objects are perceived they are decomposed into 3D set of primitives called geons, together with the skeleton structure connecting them. We present a set of guidelines for drawing variations on node-link diagrams using geon-like primitives, and provide some examples. Results from three experiments are reported that evaluate 3D geon diagrams in comparison with 2D UML (Unified Modeling Language) diagrams. The first experiment measures the time and accuracy for a subject to recognize a sub-structure of a diagram represented either using geon primitives or UML primitives. The second and third experi...