State of the art electrophysiological experiments use technical devices where an electrode–cell pair can be used to stimulate neurons and to record neuronal answers to these stimuli vice versa. 3D reconstruction of such biological technical interfaces is helpful to gain morphological insights to these interfaces. Questions like whether and how cellular structures do interact with the technical surface are important to interpret the functionality of the whole system and need high resolution imaging of the interface. Routine electron microscopical preparation methods like grinding, polishing or ultramicrotomy known from the material sciences on the one hand and biological approaches on the other hand are not valid as they can easily destroy the biological-technical interface in question due to their different composition and hardness. Only their combination with 3D FIB-SEM tomography allows for site-specific nanoanalytics of the complex device containing both soft organic matter and hard material and possessing a biological technical interface of interest considerably hidden inside the sample. Correlative light and electron microscopical investigation is easily obtained using specific sample holders that can be used in all instruments needed. Voxel sizes of less than 10 nm and fields of view of more than 40 μm are feasible, and can be adapted depending on the research question. Here we show two examples of how FIB SEM tomography can be used to investigate such cell–electrode pairs. However, the technique can be widened and used for almost any topic where soft and hard materials have to be investigated together.