Coccolithophore algae produce elaborately structured skeletons composed of sub-micrometer-scale calcite crystals. In order to understand calcite crystallization and assembly in a coccosphere with nanoscale resolution, the crystal orientation and interdigitation of the structural units were investigated by transmission electron microscopy imaging, selected-area and nano-probe electron diffraction. Focused ion beam sectioning of coccoliths of the coccolithophore species Emiliania huxleyi is used to obtain target-prepared specimens in suitable orientation. We were able to detect and analyze the V-unit, which is overgrown by the R-unit. For the V-unit the  direction points perpendicular to the coccolith plane while the  axis is tangential to the coccolith ring. The R-unit c-axis is parallel and the b-axis is perpendicular to the coccolith plane, thus confirming the R- and V-model which was based on scanning electron microscopy and optical microscopy. Furthermore we show that the distal- and the proximal shield element of an individual R-unit of a single segment are tilted by 4° ± 1° with respect to each other. This orientation change is required to obtain the flat domed character of the coccoliths, which is necessary to form the coccosphere. The orientation change between the distal- and the proximal shield element appears continuous.