Direct patterning of functional microstructures on monocrystalline silicon by mechanical micro-milling has drawn intense interests as an alternative to the conventional lithographybased technique in microelectronics fabrication. Despite the micro milling offers advantages such as versatility and low operating cost, machining induced defects such as edge chipping occur on the surface edges of a finished product and may affect its functionality. To address such challenge, a novel hybrid technique that combines mechanical machining and the deposition of a layered sacrificial structure on the silicon surface was proposed to minimise the machining induced edge chipping. In this paper, the cutting mechanism of silicon under the proposed hybrid technique has been studied by molecular dynamics simulation. Fundamental mechanisms such as material deformation, chip formation and stress behaviour are analysed.Reduction of stress intensity and machining forces has been observed when silicon was machined under the proposed hybrid conditions. The effect is believed to be contributed by thermal softening, resulted from the high cutting temperature and interfacial stress between the copper and silicon layers. In addition, machining silicon by the proposed hybrid technique also showed desirable properties which include low subsurface damages, large material removal rate and better surface finishing (Ra<0.1 nm). The results further enriched the machining theory and justified the feasibility for the proposal of such a hybrid technique.