Background: During the last few decades, increasing interest has arisen in the field of nano-machining simulations. Due to the inability of other numerical techniques to properly describe the interactions in atomistic level, Molecular Dynamics method was shown to be capable of producing sufficiently accurate results and represent the mechanisms of nano-cutting. Significant progress has been noted since the first MD studies of nano-machining and it is worthwhile to present modeling techniques and details which have been employed in the literature.Methods: A significant amount of original work in the field on MD nano-machining simulations is reviewed and presented in order to underline the advances in this field during the past few decades. Then, based on the relevant literature, a brief and concise step-by-step methodology of nanomachining processes modeling using the MD method is presented with a view to provide the beginners with a practical guide for MD modeling. For that reason, the components of each modeling step are clearly introduced to the readers and the choice of parameters according to the characteristics of each process is justified. Results: Contemporary and older MD nano-machining studies are reviewed and valuable information about both common and state-of-the-art modeling techniques is gathered. Modeling of MD processes can be structured as step-by-step methodology which leads gradually to the definition of all parameters required for an MD simulation. Methods and modeling details can be useful for the set-up of a nano-machining simulation, design of new machining processes or variants of existing ones. Conclusion: Nano-machining processes are of increasing interest for state-of-the-art industrial and scientific applications. MD method is a reliable means of simulating these processes and obtaining valuable information about the characteristics of nano-machining that are impossible to be observed by experimental work. Modeling with MD method can be viewed as a multistep methodology with each step consisting of definitions of different parts of MD model. Successful use of modeling methodology can lead to efficient and accurate simulation of nano-machining processes, as well as help the design of new ones.