In this paper, an intelligent robust controller is proposed for a class of nonlinear systems in presence of uncertainties and bounded external disturbances. The proposed method is based on a combination of terminal sliding mode control and adaptive neuro-fuzzy inference system with bee’s algorithm training. For this purpose, a sliding surface is firstly designed based on terminal sliding control method. This sliding surface is considered as input for the intelligent controller which is an adaptive neuro-fuzzy inference system and using it, terminal sliding mode control law without the switching part is approximated. In the proposed method, an intelligent bee’s algorithm is also used for updating the weights of the adaptive neuro-fuzzy inference system. Compared with fast terminal sliding mode control, the proposed controller provides advantages such as robustness against uncertainty and disturbance, simplicity of controller structure, higher convergence speed compared with similar conventional methods and chattering-free control effort. The method is applied to an atomic force microscope for nano manipulation. The simulation results show the robustness and effectiveness of the proposed method.