In this paper, the results of using a Coarse Grained Molecular Dynamics (CGMD) model to simulate the process of manipulation of nano clusters with a flexible tip are reported, and the reasons for some failures are discussed. After comparison of these results with those from a macro model, some failures of the nano manipulation process, due to damage, fracture, or crushing of tip, substrate, and nano cluster, are examined. At the end, after a parametric study of nano cluster deformations, the use of the tip cluster, ep-SP diagram, for optimal selection of the tip material, is discussed.