The control of micro- and nanoscale systems is a vital yet challenging endeavor because of their small size and high sensitivity, which make them susceptible to environmental factors such as temperature and humidity. Despite promising methods proposed for these systems in literature, the chattering in the controller, convergence time, and robustness against a wide range of disturbances still require further attention. To tackle this issue, we present an intelligent observer, which accounts for uncertainties and disturbances, along with a chatter-free controller. First, the dynamics of a carbon nanotube (CNT) are examined, and its governing equations are outlined. Then, the design of the proposed controller is described. The proposed approach incorporates a self-evolving neural network-based methodology and the super-twisting sliding mode technique to eliminate the uncertainties’ destructive effects. Also, the proposed technique ensures finite-time convergence of the system. The controller is then implemented on the CNT and its effectiveness in different conditions is investigated. The numerical simulations demonstrate the proposed method’s outstanding performance in both stabilization and tracking control, even in the presence of uncertain parameters of the system and complicated disturbances.