With the development of location based services (LBS), indoor positioning has been a popular research topic in recent years. Since global positioning system (GPS) signal suffers from severe attenuation when penetrating through solid walls, other alternatives are proposed to realize indoor positioning. Visible light communication (VLC) systems offer a practical solution. Light emitting diode (LED) is able to be modulated in high speed as a transmitter, and a photodiode (PD) is commonly a receiver to detect the optical signal strength. In VLC based indoor positioning system, LEDs are applied for both positioning and illumination purposes so that infrastructure cost and power consumption are decreased. In addition, light positioning system provides other advantages such as no electromagnetic interference and better immunity against multipath reflections. Several methods are proposed to realize indoor positioning, such as triangulation, scene analysis and proximity, which are also applicable for a VLC based system. In prior works, the height of receiver is known so that the coordinates on the horizontal plane can be calculated. In this paper, the proposed method includes two stages: the height is presumed in the prediction stage and nonlinear estimation is applied in the correction stage to realize three dimensional coordinate estimation.