In this work we present an efficient Multi Level Monte Carlo (MLMC) algorithm capable of propagating operational uncertainties, due to atmospheric variability of external aerodynamics flows and geometrical uncertainties due to manufacturing tolerances and fatigue. The technique is tested on the NACA 0012 airfoil in transonic conditions and a two compression ramps hypersonic scramjet intake configuration. The efficiency of the proposed MLMC algorithm in terms of accuracy versus overall computational cost is compared to a standard MC method.