Optical communication systems in free space require a coarse and fine alignment system to align the receiver and transmitter. In general a coarse alignment is not entirely accurate to transmit the laser beacon in the exact direction of the visible field of the camera. During this process, some algorithms such as the raster, spiral and raster spiral scan algorithm can be used to find the spot of the laser beacon. Applications that require to transmit data in form of polarization signals, such as quantum cryptography, requires a polarisation bases alignment system to transmit and receive the photons. In this paper we present a fine alignment system using a polarised laser beacon. The system proposed was subdivided into a coarse and fine alignment system. The coarse alignment was implemented by using the GPS to acquire the geographical position of the transmitter, receiver and a reference point. The fine alignment was achieved by using a polarised laser beacon from the receiver to the transmitter and a camera located on the transmitter side. The algorithm presented was capable of excluding the background noise. Furthermore the polarisation of the laser beacon was used to align the polarisation bases of the transmitter and the receiver.