Manufacturing at the atomic scale is the next generation of the industrial revolution. Atomic and close-to-atomic scale manufacturing (ACSM) helps to achieve this. Atomic force microscopy (AFM) is a promising method for this purpose since an instrument to machine at this small scale has not yet been developed. As the need for increasing the number of electronic components inside an integrated circuit chip is emerging in the present-day scenario, methods should be adopted to reduce the size of connections inside the chip. This can be achieved using molecules. However, connecting molecules with the electrodes and then to the external world is challenging. Foundations must be laid to make this possible for the future. Atomic layer removal, down to one atom, can be employed for this purpose. Presently, theoretical works are being performed extensively to study the interactions happening at the molecule–electrode junction, and how electronic transport is affected by the functionality and robustness of the system. These theoretical studies can be verified experimentally only if nano electrodes are fabricated. Silicon is widely used in the semiconductor industry to fabricate electronic components. Likewise, carbon-based materials such as highly oriented pyrolytic graphite, gold, and silicon carbide find applications in the electronic device manufacturing sector. Hence, ACSM of these materials should be developed intensively. This paper presents a review on the state-of-the-art research performed on material removal at the atomic scale by electrochemical and mechanical methods of the mentioned materials using AFM and provides a roadmap to achieve effective mass production of these devices.