Atomic and close-to-atomic scale manufacturing (ACSM) aims to provide techniques for manufacturing in various fields, such as circuit manufacturing, high energy physics equipment, and medical devices and materials. The realization of atomic scale material manipulation depending on the theoretical system of classical mechanics faces great challenges. Understanding and using intermolecular and surface forces are the basis for better designing of ACSM. Transformation of atoms based on scanning tunneling microscopy or atomic force microscopy (AFM) is an essential process to regulate intermolecular interactions. Self-assemble process is a thermodynamic process involving complex intermolecular forces. The competition of these interaction determines structure assembly and packing geometry. For typical nanomachining processes including AFM nanomachining and chemical mechanical polishing, the coupling of chemistry and stress (tribochemistry) assists in the removal of surface atoms. Furthermore, based on the principle of triboelectrochemistry, we expect a further reduction of the potential barrier, and a potential application in high-efficiency atoms removal and fabricating functional coating. Future fundamental research is proposed for achieving high-efficiency and high-accuracy manufacturing with the aiding of external field. This review highlights the significant contribution of intermolecular and surface forces to ACSM, and may accelerate its progress in the in-depth investigation of fundamentals.