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Models capable of accurate simulation of the microcantilever dynamics coupled with complex tip-sample interactions are essential for interpretation of the imaging results in non-contact atomic force microscopy (AFM). In the present research, a combination of finite element and molecular dynamics methods are used for modelling the AFM system to overcome the drawbacks of conventional approaches that use a lumped system with van der Waals interaction. To illustrate the ability of the proposed scheme in providing images with atomic resolution, some simulations have been performed. In the conducted simulations, a diamond tip is interacting with nickel samples having different surface plane directions. The results demonstrate the effectiveness of the proposed modelling method for measuring the surface topography with appropriate contrast and atomic details.