The friction is one of the nonlinearities to be considered in the precise position control of a system which has electromechanical components. The friction has complicated nonlinear characteristics and depends on the velocity, the position and the time. The conventional fixed friction compensator and the controller based on linear control theory may cause the steady state position error or oscillation. The plant to be controlled in this study is a positioning system with a linear brushless DC motor(LBLDCM). The system behaves like a 4th-order model including the compliance and the friction. In this study, the plant model is simplified to a 2nd-order model to reduce the computation in on- line estimation. Also, to reduce the computation time, only the friction is estimated on-line while the mass and the viscous damping coefficient are fixed to the values obtained from off-line estimation. The validity of the proposed scheme is illustrated with the computer simulation and the experiment where the friction is compensated by using the estimation.