The tracking control problem of a class of nonlinear systems via inverse dynamics method is addressed. The motivation for the study stems from the need to control practical systems arising from aerospace and mechanical engineering. Because modeling uncertainties and external disturbances are always present in these systems, inverse dynamics technique is not applicable directly. A compensated inverse dynamics approach is proposed to account for the effect of uncertainties. The compensation is achieved by adaptive and robust schemes. Application of the proposed strategy to the vibration suppression of a two-bay flexible truss structure is presented.