Future trends in materials and devices are strongly based on novel fabrication methods that allow for mass production with low cost and high throughput. Such methods must be finely optimized to achieve nanometric control without incurring in high costs. This can be achieved by developing a process that reduces the number of steps required, as well as by reducing the amount of human involvement in the process, which would increase the quality and reproducibility of the output. But the improvement of fabrication technologies cannot be optimized without considering the materials desired, along with its most fundamental chemical and physical properties. Hence, to successfully design the instrumentation needed for novel fabrication technologies with nanometric precision, the design methodology must consider multiple different subjects related to the chemistry, physics, mechanics, electronics and automation, all working together to achieve the desired objective. In this doctoral work, such design methodology was implemented with a diverse number of tools and approaches to successfully optimize a nanofabrication method called Spatial Atomic Layer Deposition (SALD) to deposit thin films of a material that has potential applications as a component of non-silicon solar energy devices, photoelectrochemical water splitting devices, and thin film transparent electronics, among others: cuprous oxide (Cu2O ). Regarding the fabrication technology and the mechatronic design, SALD is a promising fabrication technique that allows fabrication of thin films with nanometric precision and with the ability to control their mechanical, electrical and crystallographic properties. Furthermore, the SALD approach used in this thesis and in the Laboratoire des Matériaux et du Génie Physique (LMGP) works in the open-air (no deposition chamber), and thus is potentially an industrial-compatible approach for large area, homogeneous thin film fabrication with a high throughput. Additionally, SALD can be used with conditions that make it compatible with flexible substrates and with rollto- roll (R2R) approaches. Finally, SALD provides flexibility on the deposition process so that it can be tuned to obtain different properties on the films fabricated with minimal change in the instrumentation. In this thesis, some of the potential benefits of the flexible parameters of the SALD system are explored and the impact of some of them on fabricated films is presented. Using Computational Fluid Dynamics (CFD) simulations, the fluid mechanics phenomena that occur during the deposition process in the SALD system were analyzed for different configurations of the reactor. The influence on the film properties were studied and validation with experimental depositions were performed. Afterwards, using the knowledge and guidelines obtained with the CFD simulations, and in order to lower the cost and complexity of modifying some of the mechanical components of the system, a workflow including Computer Aided Design (CAD) and additive manufacturing (also known as 3D printing) was established at the LMGP for the fabrication of one of the main components of the SALD system at LMGP: the deposition head. The use of additive manufacturing has followed a rapid increase on applications, and, in this work, it is the first time that such innovative fabrication technique is applied to thin-film nanofabrication processes, providing numerous potential applications in the field. In this thesis, such workflow is shown and explained, and the guidelines learned, and limitations discovered are presented as well. Finally, after making some modifications on the system and adding the necessary components such as new heating systems and containers for the needed precursor, Cu2O was successfully deposited with the SALD method. Cu2O is one of the few materials with promising electronic properties as a p-type transparent semiconductor. It is also a material that allows for mass production, if coupled with an industrial-compatible fabrication method (such as SALD), thanks to its non-toxicity, its chemical and environmental stability and its earth abundance. Here, the fabricated Cu2O films using the SALD system at LMGP are reported, and their p-type conductivity and crystallography are analyzed. In the work done during this doctoral project, a systematic approach was used to analyze, adapt and optimize the SALD system at LMGP for the deposition of Cu2O. Using CFD simulations, CAD tools, 3D printing and automation, the whole process was successfully installed in the system and highly conductive Cu2O films can be now deposited their further study or for their integration in numerous types of devices. Furthermore, the results of this work provide initial guidelines for the industrial design of an SALD-based high-throughput fabrication system, in which the design of its components is optimized for each material desired. Such design approach, combined with the flexibility and low cost of the SALD, the flexibility of the mechanical design and fabrication of some of its components, and the speed of the deposition procedure, make this work also useful to further increase the amount of materials compatible with SALD, as well as to further develop the SALD methodology into innovative fabrication processes of materials and devices.