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Atomic force microscopes have been widely used for nanomanipulation in recent years. Since the task of nanomanipulation is tedious for humans, and it is desirable to have a proficient process, controlled manipulation in nanoscale is an extremely important issue. In this Letter, a compatible nanomanipulation model consisting of all effective phenomena in nanoscale for manipulation by variant substrate motion profile is proposed to perform an accurate manipulation task. The dynamic model of nanoparticle displacement utilises the Lund-Grenoble friction model, depicting the true stick-slip behaviour of the nanoparticle in manipulation. The sliding mode control approach is used to overcome the challenges in piezoelectric substrate motion control. It compensates drift, hysteresis and other uncertainties, to provide the desired substrate motion trajectory with the desired error dynamics. The final automated process provides satisfactory results with respect to experiments and enables automated manipulation, with associated savings in time and labour, and increased complexity of the resulting created structures.