The structural singular value (μ) analysis method of the system uncertainty of flexible structures is presented. Due to the modal truncation and parameter uncertainty, the structural model used for control misses out on high frequency dynamics and causes parameter smearing. The unmodeled high frequency dynamics of the flexible structure is studied as additive uncertainty and multiplicative uncertainty of nominal model. The parameter perturbation in modal space is used to capture the uncertainty in state space. The structural singular value method is used to characterize the robust stability and performance of the controller for structural model with uncertainty. It is conclused that the modeling method for flexible structures and μ analysis of the control systems are valid by a sample problem.