Two-dimensional materials have attracted significant interest and investigation since the marvellous discovery of graphene. Due to their unique physical, mechanical and optical properties, van der Waals (vdW) materials possess extraordinary potential for application in future optoelectronics devices. Nano-engineering and nano-manufacturing in the atomically thin regime has further opened multifarious avenues to explore novel physical properties. Among them, moiré heterostructures, strain engineering and substrate manipulation have created numerous exotic and topological phenomena such as unconventional superconductivity, orbital magnetism, flexible nanoelectronics and highly efficient photovoltaics. This review comprehensively summarizes the three most influential techniques of nano-engineering in 2D materials. The latest development in the marvels of moiré structures in vdW materials is discussed; in addition, topological structures in layered materials and substrate engineering on the nanoscale are thoroughly scrutinized to highlight their significance in micro- and nano-devices. Finally, we conclude with remarks on challenges and possible future directions in the rapidly expanding field of nanotechnology and nanomaterial.