Instrumented umanned aerial vehicles represent a new way of measuring turbulence in the atmospheric boundary layer. However, autonomous measurements require control methods with disturbance-rejection and altitude command-following capabilities. Filtered dynamic inversion is a control method with desirable disturbance-rejection and command-following properties, and this controller requires limited model information. We implement filtered dynamic inversion as the pitch controller in an altitude-hold autopilot. We design and numerically simulate the continuous-time and discrete-time filtered-dynamic-inversion controllers with anti-windup on a nonlinear aircraft model. Finally, we present results from a flight experiment comparing the filtered-dynamic-inversion controller to a classical proportional-integral controller. The experimental results show that the filtered-dynamic-inversion controller performs better than a proportional-integral controller at certain values of the parameter.