Too much effort has been done for manipulating individual atoms, using nano-manipulators and Scanning Tunneling Microscopes (STM). On the other hand, characterization and manipulation of nano-flows is of great concern. In the current work a molecular valve has been considered, which is made up of six atoms placed on the circumstance of a circle. A fuzzy controller has been designed for controlling the diameter of this molecular valve. The designed fuzzy controller used singleton fuzzifier, Mamdani inference engine, center average defuzzifier and exponential membership functions. A model based on the classical Molecular Dynamics (MD) is used for modeling the nano-system and passing the states to the fuzzy controller. Then the fuzzy controller sets the actuators positions in order to control the diameter of the molecular valve. It has been shown that the designed controller can control the radius with an appropriate accuracy. Dimensionless equations of motion are used for designing the controller; therefore the designed controller is versatile and applicable to all the cases that the interactions between actuators and molecules can be modeled by Lennard-Jones potential. Using such a controller makes the molecular valve become applicable in the real world which has great applications such as drug delivery and controlling nano-flows with single molecule accuracy.