Finite element models of dynamic systems can be updated in two stages. In the first stage, mass and stiffness matrices are updated neglecting damping, and in the second stage, damping matrices are estimated with the mass and stiffness matrices fixed. Three methods to estimate damping matrices for this purpose are proposed in this paper. The methods include one for proportional damping systems and two for non-proportional damping systems. Method 1 utilizes orthogonality of normal modes and estimates damping matrices using the modal parameters extracted from the measured responses. Method 2 estimates damping matrices from impedance matrices which are the inverse of FRF matrices. Method 3 estimates damping using the equation which relates a damping matrix to the difference between the analytical and measured FRFs. The characteristics of the three methods are investigated by applying them to simulated discrete system data and experimental cantilever beam data.