At the interface between science and engineering, there is the field of biomimicry: Innovations inspired by the observation of natural, evolutionary optimized biological structures and processes. To understand the challenges of biomimicry, the concept of “Molecular Tectonics” is particularly useful. It describes how different self-assembling processes are spatially and dynamically integrated to form successively more complex structures. This integration makes it difficult to isolate the underlying mechanisms, which are often on the scale of individual molecules. Molecular biomimicry therefore critically depends on the observation of natural systems at the molecular scale. Advances in scanning probe microscopy have enabled the study of molecular self-assembly in unprecedented detail. However, many of these advances critically depend on the use of Ultra High Vacuum (UHV) conditions. To study natural systems at the molecular scale, a transition from UHV towards solvated systems is required. In the first part of this thesis, small synthetic peptides are used as model system for molecular self-assembly. The self-assembly of peptides at interfaces has been studied by systematically varying the chemical structure and deposition method. By using ElectroSpray Ion Beam Deposition (ES-IBD) as well as in situ drop casting, the self-assembly at the solid-vacuum interface (UHV conditions) and at the solid-liquid interface was directly compared. This comprehensive study on the effect of solvent, structure and deposition method on the assembly of peptides at gas-solid and solid-liquid biointerfaces has shown that the same AcFA5K peptide can organize into various structures, from β-sheets to tubular and globular assemblies, depending on their local environment. The study of molecular self-assembly was extended to 2D protein crystals. By using high-speed and high-resolution and Atomic Force Microscopy (AFM), it was possible to resolve both spatially and dynamically the mechanisms involved in S-layer self-assembly at the solid-liquid interface, such as monomer adsorption, condensation into high-density clusters, crystallization and finally conformational changes of existing S-layer crystals. In the second part of this thesis, the integration of different self-assembling systems is explored and their functional properties are investigated. It combines the concepts of self-assembly and molecular tectonics. Self-assembled striped PS-b-PEO block copolymer (BCP) thin film substrates were used to confine and align S-layer self-assembly, without affecting the internal structure. Furthermore, the nucleation rate and S-layer growth was greatly enhanced on PS-b-PEO substrates, compared to the pure PS or PEO constituents. The hierarchical use of different self-assembling systems can be seen as a functional approach to the concept of molecular tectonics. The catalytic properties of S-layers regarding the formation of CaCO3 were studied. By studying the catalytic properties of S-layers ex vivo, their role can be investigated independently from the internal metabolism of their parent bacteria. Synchrotron based in situ X-ray Absorption Spectroscopy (XAS) and AFM are combined with continuous flow conditions, demonstrating that S-layers are able to stabilize amorphous forms of CaCO3 and catalyze the nucleation of calcite at extremely low supersaturations.