Phase-shifting profilometry combined with Gray-code patterns projection has been widely used for 3D measurement. In this technique, a phase-shifting algorithm is used to calculate the wrapped phase, and a set of Gray-code binary patterns is used to determine the unwrapped phase. In the real measurement, the captured Gray-code patterns are no longer binary, resulting in phase unwrapping errors at a large number of erroneous pixels. Although this problem has been attended and well resolved by a few methods, it remains challenging when a measured object has step-heights and the captured patterns contain invalid pixels. To effectively remove unwrapping errors and simultaneously preserve step-heights, in this paper, an effective method using an adaptive median filter is proposed. Both simulations and experiments can demonstrate its effectiveness.