The main objective of this project is to obtain a controller design methodology for uncertain, nonlinear, mechanical and aerospace systems which contain flexible components. Using a singular perturbation approach, the first phase of the research considers controllers which are designed assuming certain components to be rigid, and then investigates the effect of flexibility in the previously assumed rigid components on the controller performance. In the second phase of the research, all flexibilities are taken into account in the controller design; currently known results on the control of uncertain systems are extended to systems whose uncertainties satisfy less restrictive structural conditions than the previous conditions. In both phases, the design of the controllers and the analysis of their performance are based on Lyapunov functions.