Three-dimension molecular dynamics (MD) simulations is employed to investigate the ultraprecision machining of single crystal silicon with structured nanoscale diamond tool fabricated by laser. The advantages and disadvantages of diamond machining using structured tools are discussed in comparison with those, of using non-structured tools. The von Mises stress distribution, hydrostatic stress distribution, atomic displacement, stress, the radial distribution function, cutting forces, frictional coefficient, subsurface temperature and potential energy during the nanometric machining process are studied. A theoretical analysis model is also established to investigate the subsurface damage mechanism by analyzing the distribution of residual stress during the nanoscale machining process. The results show that a structured nanoscale tool in machining brittle material silicon causes a smaller hydrostatic stress, a less compressive normal stress sigma(xx), and sigma(yy), a lower temperature and a smaller cutting force. However, the structured nanoscale tool machining results in smaller chip volume and more beta-silicon phase. Besides, the friction coefficient for tool with V-shape groove is smaller than those for non-structured tools and other structured nanoscale tools. This means that the tool with V-shape groove can reduce the resistance to cutting during the nanoscale machining process. In addition, the results also point out that the potential energy of subsurface atoms and the number of other atoms for pyramid-structured tool are much smaller than those of using non-structured tools and other structured nanoscale tools. (C) 2016 Elsevier B.V. All rights reserved.