This book contains a research report on one of the most important factor “Wind” affecting the autonomous flying of unmanned aerial vehicles. The current research focuses on current wind estimation methods used in commercial off the shelf autopilot boards. The current algorithms are simulated for robust real life wind conditions for a fixed wing aircraft using Software in The Loop Simulator (SITL) setup at Arizona State University. The different flight paths are simulated for near accurate flight dynamics model. The similar experiments with are performed using Skywalker, remote controlled aircraft. The Skywalker is equipped with Ardupilot Mega 2.6 autopilot board. The SITL simulated mission plan was flown onboard with Skywalker airplane. The results shown that the inability of flying through windy condition due to inaccuracy in wind measurement algorithm currently being used. The research work also suggests some newer techniques for estimation and navigation algorithms.