Nowadays, guidance and control methods have very important usage in various fields as agricultural applications, topography and surveying, hostilities and wars. A complete Autopilot system is composed of a path planner system, referring to the next point of the trajectory of the vehicle's motion, a guidance system, which represents commands to the control system using path planner information, and a control system generating control commands to the control surfaces. Navigation systems make feedback of the control loop. In this thesis after surveying on navigation and guidance methods used in aircraft autopilot systems, we completely model a real UAV with complete details and its real parameters in the MATLAB/Simulink environment. The complete generated 4x4 nonlinear model will be controlled, using robust control methods for each 2x2 plant separated from the large model, named Lateral and Longitudinal systems.