To understand the structure of molecules, various computational methodologies have been extensively investigated such as the Voronoi diagram of the centers of atoms in molecule and the power diagram for the weighted points where the weights are related to the radii of the atoms. For a more improved efficiency, constructs like an $alpha$-shape or a weighted $alpha$-shape have been developed and used frequently in a systematic analysis of the morphology of molecules. However, it has been recently shown that $alpha$-shapes and weighted $alpha$-shapes lack the fidelity to Euclidean distance for molecules with polysized spherical atoms. We present the theory as well as algorithms of $eta$-shape and $eta$-complex in $mathbb{R}^3$ which reflects the size difference among atoms in their full Euclidean metric. We show that these new concepts are more natural for most applications and therefore will have a significant impact on applications based on particles, in particular in molecular biology. The theory will be equivalently useful for other application areas such as computer graphics, geometric modeling, chemistry, physics, and material science.