Biomolecular functional complexes often serve as inspiration for the development of artificial molecular nanostructures. The functionality of the biomolecular structures is based on complex and adaptable binding motifs that have evolved over billions of years. The detailed understanding of the underlying interactions is pivotal for the rational design and development of new materials, but often difficult to achieve as it requires submolecular resolution. In this thesis, I show how the molecular imaging of biopolymers by scanning tunneling microscopy (STM) and low-energy electron holography (LEEH) contributes to deciphering the structures and the respective binding motifs. These high-resolution imaging methods only perform well on surfaces in ultra-high vacuum (UHV) and for chemically identified species. Thus, electrospray ion beam deposition (ES-IBD) is essential for the controlled deposition for non-volatile species in UHV. The first part of the thesis focuses on the characterization of the disaccharides as smallest representatives of polysaccharides. Deposited by ES-IBD, the first high-resolution STM characterization of this molecular class on a surface in UHV is performed. The disaccharides sucrose and trehalose can be distinguished as they exhibit specific self-assembly motifs and are imaged differently. For sucrose, the two monosaccharide building blocks are resolved, highlighting the impact that high-resolution imaging by STM might have in the future for the clarification of unknown sequences by identifying branching points. In the second part of the thesis, peptides are employed as building blocks for novel structures on the surface. A combined approach of STM imaging with modeling by MD and DFT is applied to identify the binding motifs and the underlying specific interactions. Understanding of the binding motifs of the decapeptide angiotensin-I on Au(111) enables the design of a long-ranged ordered honeycomb network by manipulating the sequence to the octapeptide angiotensin-II. Representing a further binding motif that is often employed in catalytically active peptides, peptide-metal complexes are investigated on the surface showing a significant influence on the peptide structure. Based on the long-range ordered network for the pure angiotensin-II, we find that the introduction of a metal coordination center makes the molecular structure more compact and thus reduces the intermolecular interaction sites yielding an assembly of reduced dimensionality. In the last part, the proof of principle is presented that LEEH, empowered by the ES-IBD sample preparation, is able to image single folded proteins on free stranding ultra-clean graphene and might therefore provide protein structures without averaging. To this end, native mass spectrometry is adopted to ES-IBD for the deposition of folded proteins (cytochrome C, bovine serum albumin) and protein complexes (hemoglobin). In conclusion, the versatile deposition of biopolymers by ES-IBD enables UHV based single molecule imaging techniques for a range of different samples, starting from imaging the sequence and characterizing 2D nanostructures of biomolecules by STM to 3D folded protein complexes imaged by LEEH. High-resolution imaging opens new perspectives for structure determination, such as the branching points of polysaccharides and the 3D structure of single proteins. Moreover, a detailed understanding of binding motifs is crucial for the rational design of new nanostructures.