One of the key factors in the assembly of nanoclusters; is the precise positioning of them by a manipulation system. Currently the size of clusters used as building blocks is shrinking down to a few nanometers. In such cases, the particle nature of matter plays an important role in the manipulator/cluster/substrate interactions. Having a deeper insight to the aforementioned nano-scale interactions is crucial for prediction and understanding of the behavior of nanoclusters during the positioning process. In the present research, 2D molecular dynamics Simulations have been used to investigate Such behaviors. Performing planar simulations can provide a fairly acceptable qualitative tool for our purpose while the computation time is greatly reduced in comparison to 3D Simulations. The system consists of a tip, Cluster and substrate. The focus of the present research is on ultra-fine metallic nanoclusters. To perform this research, Nose-Hoover dynamics and Sutton-Chen interatomic potential will be used to investigate the behavior of the above system which is made from different transition metals. The effects of material type, tip form and manipulation strategy on the Success of the process have been investigated by planar molecular dynamics. Such qualitative simulation studies can evaluate the chance of success of a certain nanopositioning scenario regarding different working conditions before consuming large-scale computation time or high experimental expenses. (C) 2008 Elsevier B.V. All rights reserved.