Atomic force microscopy (AFM) tip-based nanomachining technique has been proved as a powerful method to fabricate nanostructures. The nanomachining approach proposed in this study offers a new concept to improve the width resolution and processing efficiency of AFM tip-based nanofabrication techniques. The method uses a dual-tip probe and single-crystal copper is used as the sample material. A depth prediction model is developed for the nanoscratching process using the dual-tip probe. The results obtained by nanoscratching tests show that symmetrical three-dimensional (3D) nanostructures composed of two large pile-ups and one small hump can be machined. The model predicts the machined nanostructure depth accurately when the machined depth reaches approximately 40 nm; the blunt tip and the inclined inner wall of the dual-tip gap may be the main reasons for the inaccurate predictions at smaller machined depths. Moreover, molecular dynamics (MD) simulation is also used to investigate the scratching process with the dual-tip probe. The simulation results obtained agree well with the experimental results.