In this paper we consider an inverse problem for a damped vibration system from the noisy measured eigendata, where the mass, damping, and stiffness matrices are all symmetric positive definite matrices with the mass matrix being diagonal and the damping and stiffness matrices tridiagonal. To take into consideration the noise in the data, the problem is formulated as a convex optimization problem involving quadratic constraints on the unknown mass, damping, and stiffness parameters. Then we propose a smoothing Newtontype algorithm for the optimization problem, which improves a pre-existing estimate of a solution to the inverse problem. We show that the proposed method converges both globally and quadratically. Numerical examples are also given to demonstrate the efficiency of our method.