Exact geometric description, numerical analysis and comparison of microscopic objects such as the frustules of diatoms are of increasing importance in basic research (e.g. functional morphology, taxonomy and biogeochemistry). Similarly, applied research and product development in the fields of lightweight construction and nanotechnology can benefit from machine-readable data of such structures. This paper presents a new method to combine data from scanning electron microscopy and confocal laser scanning microscopy to generate exact three-dimensional models of diatom frustules. We propose a method to obtain a high quality mesh for subsequent analysis through finite element analysis, for example, for biomechanical research on diatom frustules. A specific lightweight value as a universal tool to describe and compare the biomechanical quality of microscopic objects is introduced. Our approach improves the precision of three-dimensional reconstructions, but the generation of usable finite element meshes from complex three-dimensional data based on microscopic techniques requires either a transformation of grid points into elements or smoothing algorithms. Biomechanical analyses of differently obtained models indicate that more complex three-dimensional reconstructions lead to more realistic results.