In this paper, we propose the model based control system design for autonomous flight and guidance control of a small-scale unmanned helicopter. A small-scale unmanned helicopter has been studied with fuzzy and neural network theory, but it is not so good performance for unmodel based control to stabilize it. For this reason, we design a mathmetical model (Mettler's model) and a model based controller for a small-scale unmanned helicopter system. In order to realize a full autonomous small-scale unmanned helicopter, we have designed the attitude controller and trajectory controller with kalman filter based LQI for a small-scale unmanned helicopter. The characteristic of the attitude closed loop dynamics is taken into consideration to design a trajectory controller. By way of the simulations and experiments, it has been clarified that the proposed scheme for attitude control and guidance control is very useful.