A novel approach based on molecular dynamics (MD) simulation has been proposed for the first time with the focus on quantifying the minimum feed (MF) in atomic force microscope (AFM) based nanochannel fabrication. This approach involves a coarse-to-fine criterion to determine MF so that regular nanochannel patterns can be obtained. The method is first introduced step by step and then confirmatory test is performed to demonstrate the capability of this contour-based method. MF judging studies are also performed systematically in which they vary in the aspects of scratching depth, tip angles, and tip shapes. Dislocations generation, surface quality, and scratching forces in the initial and subsequent scratches are investigated in detail. This method can overcome the drawbacks of high cost and low efficiency in experimental studies. Furthermore, our method sheds light on the manufacturing technique of nanochannels, which can help to obtain the surface morphologies with higher quality than traditional approaches. (C) 2016 Elsevier B.V. All rights reserved.