The rational synthesis of novel materials requires the control over the arrangement of matter in order to meet the desired properties for applications and devices. Ultimately, control means to define the place of each atom and determine its chemical state, as well as being able to confirm the result in a measurement. Control at the atomic level can be achieved with scanning tunneling microscopy (STM), both in imaging and atomic manipulation. The latter, however, can never be used in meso- or even macroscopic material synthesis. Self-ordering phenomena determines atomic control in material synthesis as well, observed for instance in protein folding or in molecular beam epitaxy (MBE) technology. In both cases the atomically determined arrangement of the atoms in the structure is controlled only by environmental parameters that steer the self-ordering phenomena. In this thesis I show that electrospray ion beam deposition (ES-IBD) or ion soft-landing is a material processing technique, which combines and even extends the level of control offered by MBE. It is demonstrated that a vast range of complex organic materials including peptides and proteins is now available to ultrapure vacuum processing and moreover completely novel schemes of controlling self-ordering processes are provided. In-situ STM is applied to investigate the structure formation of complex molecules deposited by ES-IBD on well-defined, clean, and atomically flat surfaces in ultrahigh vacuum at the greatest detail. This allows us to explore the novel control features that are intrinsic to the ES-IBD deposition process like online coverage monitoring, deposition energy control, and mass-selection to select charge states or reactive species. The molecules studied here include organic molecular salts, dye molecules, reactive polymer building blocks, and finally peptides and proteins. Crystalline layer-by-layer as well as island growth was observed and revealed the equivalence to conventional MBE growth. On the basis of these deposition experiments the crucial influence of clusters in the ion beam for high material flux was discovered. Furthermore, it was found that the chemical state of the molecule is a key factor for the deposition result as chemical reactions can be induced or the self-assembly behavior can be altered. Alongside the capability to handle also extremely reactive molecules, the feasibility to control chemical reactions occurring as a result of an external stimulus to a specifically selected reactive species is demonstrated. Employing the control parameters that are specific to ES-IBD like charge state selection and deposition energy to complex biomolecules opens up new perspectives for vacuum deposition. In addition to the self-assembly governed by the molecule-substrate and molecule-molecule interaction, it was possible to actively steer the structure formation of proteins by influencing their stiffness and their reactivity through their charge state as well as by the deposition energy, parameters intrinsic to the ES-IBD method. Hence, electrospray ion beam deposition is indeed a tool to prepare well defined surface coatings at highest level of control and complexity. To be relevant for industrial applications, the performance of the system has to be further improved, most importantly in terms of deposition rate. In general, ES-IBD enables new approaches for the growth of functional coatings but also serving as perfect sample preparation tool for the characterization of complex molecules on the atomic scale by scanning probe or more general surface science methods.