With the increasing technological growth, the need for more precise and accurate level of manufacturing is inevitable. This enhanced precision helps to reduce the size of transistors and other integrated circuit components for improved functionality of devices. Atomic/close-to-atomic scale manufacturing (ACSM) is a necessity to achieve this size reduction. Prof. Fengzhou Fang’s team at the Centre of Micro/Nano Manufacturing Technology (MNMT) aims in developing fundamental aspects and perspectives to realise ACSM. Since this research is in its early stage, a relevant study is performed both in theoretical, with the aid of Density Functional Theory (DFT) and experimentation using Atomic Force Microscope (AFM). For developing atomic scale devices, the use of molecules are important since they are defect free and can reduce the device size considerably. However, the difficult of attaching molecules to the electrodes is a daunting task. For this, the effect of interactions taking place at the electrode-molecule junction need to be explored. Periodic Energy Decomposition Analysis (pEDA) is a recently modified method to find the bonding interactions happening between two fragments. This provides information on different types of bonding, which can be repulsive or attractive, when two fragments are brought together. A novel idea of combining pEDA and electronic transport studies to improve the development of molecular devices is presented in this paper. Moreover, this study can lead to the following aspects of molecular device fabrication. Firstly, the importance of electronic transport and conduction across the molecular junction largely depends on the bonding between electrode material and the molecule. Secondly, the selection of molecule and the electrode material is crucial for a stable and robust connection for the device functionality and finally. The point of attachment should be a single atom so that the influence of neighbouring atoms in interfering with the smooth flow of current can be reduced. This paper provides detailed information on the former two and urges the researchers to find ways to achieve the latter by atomic scale material removal. Hence, a link between pEDA and electronic transport not only helps in molecular device development, but also, pave ways for realising ACSM methods.