This paper describes the design intelligent based nonlinear controller for three dimensions joint dental robot manipulators in presence of uncertainty. Three-dimension joint dental robot manipulator has some important challenges such as nonlinearity, multi-input multi-output (MIMO), uncertainty in dynamic formulation, and coupling effect. To eliminate the effect of these challenge linear filter PID controller is introduce in this research. However, this controller has some advantages in certain condition but in uncertainty, it has problems. To improve this technique in presence of uncertainty, minimum rule base PID like fuzzy controller is introduced. This method reduces the rise time, steady state error and improves the trajectory performance in uncertain condition. Stability and robustness improve in proposed method as well reduce the number of rule base.