In this paper, the modeling and simulation of manipulation of carbon nanoparticles have been investigated. The geometry plays a significant role in the dynamic behavior of nanoparticles manipulation and the evaluation of different geometric shapes of nanoparticles in this process is very important. To examine the geometry effects, the manipulation of a different kind of the nano-carbon allotropes has been studied. Furthermore, the manipulation of carbon nanotubes with different diameter has been simulated. For this purpose, the molecular dynamics method has been used to improve our knowledge and understanding about the nanomanipulation processes and dynamics. In the manipulation of carbon allotropes, the results indicated that more spherical allotrope Modes away, the easier manipulation process occurred and the forces on the probe have been reduced; this is due to the curvature of tip and nanoparticle. The results of nanotubes manipulation showed that increasing the diameter of the nanotube causes to increase the force on the probe. The indentation depth was extracted for each nanotube during the manipulation process. The results indicated that the indentation depth increases versus diameter increasing. According to the application of carbon-based structures and nanotubes as the drug carriers in medicine, such this simulation studies can reduce time and cost of experimental projects in this field.