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To understand the deformation and removal mechanism of material on nano-scale and at ultralow loads, a systemic study on AFM micro/nano-machining on single crystal silicon is conducted. The results indicate that AFM nanomachining has a precisely dimensional controllability and a good surface quality on nanometer scale. A SEM is adopted to observe nano-machined region and chips, the results indicate that the material removal mechanisms change with the applied normal load. An XPS is used to analyze the changes of chemical composition inside and outside the nano-machined region respectively. The nano-indentation which is conducted with the same AFM diamond tip on the machined region shows a big discrepancy compared with that on the macro-scale. The calculated results show higher nano-hardness and elastic modulus than normal values. This phenomenon can be regarded as the indentation size effect(ISE).