In this research a relatively large area of nano-hole arrays is reconstructed in 3D and the surface properties computed from the DEM are analysed as shown in Table 1. The results show that two kinds of imperfections make the surface different from the ideal shape. First, the surface has a wavy shape with peaks and valleys which cannot be detected using a single SEM image. Valleys are due to the embedment of nanospheres to the photoresist by dozens of nanometres. This is obtained from the comparison of nanosphere’s diameter and the height difference between top surface of nanospheres and the bottom surface, which is presented in Fig. 5. In addition to the waviness of the surface, some areas are up and down which could be a result of uneven UV exposure in the fabrication process. These ups and downs are illustrated in Fig. 6. These two kinds of imperfections are likely to have influence to subsequent nano-manufacturing processes, especially to nanoimprinting. In nano-imprinting, an uneven surface will cause uneven pressure and result in uneven patterns. The irregularities of the master will also be copied to the subsequent products. These problems will effectively compromise the quality of subsequent fabrication.