In this paper, we present a hardware in the loop simulation of our proposed multi-surface sliding control (MSSC) for trajectory tracking of 6 degrees of freedom (6-DOF) inertia coupled aerial vehicles with multiple inputs and multiple outputs (MIMO). Using MSSC on MIMO autonomous flight systems creates confluent control that can account for both matched and mismatched uncertainties, system disturbances and excitation in internal dynamics. The control law is implemented on an onboard computer and is validated though Hardware-In-the-Loop (HIL) simulations, between the hardware and the flight simulator X-Plane, which simulates the unmanned aircraft dynamics, sensors, and actuators. Simulation results are presented to validate the analysis.