Visible light communication systems are rapidly growing research areas with wide applications ranging from illumination and data communication. To achieve high data rates in such systems, a number of techniques have been employed such as equalization of transmission signals, deployment of complex data modulation and the use of multiple input multiple output (MIMO) systems. However, security in wireless telecommunication systems is a common concern. This paper proposes a secure MIMO-VLC system that relies on the position of the user by incorporating a new modified version of the Rivest-Shamir-Adleman (RSA) technique for encrypting the transmitted data in the Media Access Control (MAC) layer. The performance of the positioning method is evaluated showing a positioning accuracy of less than 5cm for a signal-to-noise ratio (SNR) of 15 dB. Furthermore, the ability of the proposed system to control the size of the encrypted cell, depending on the application environment, is demonstrated.