This paper proposes an atomic force microscope (AFM) based force controller to push nanoparticles on the substrates since it is tedious for human. A block phase correlation-based algorithm is embedded into the controller for compensating the thermal drift during nanomanipulation. Further, a neural network (NN) is employed to approximate the unknown nanoparticle and substrate contact dynamics including the roughness effects. Using the NN-based adaptive force controller the task of pushing nanoparticles is demonstrated. Finally, using the Lyapunov-based stability analysis, the uniform ultimately boundedness (UUB) of the closed-loop signals is demonstrated