In a lidar system an accurate transmitter-receiver alignment is essential for correct results. Usually this optical adjustment is time consuming and requires the intervention of highly qualified personnel. As a solution to this problem, a fast and precise automatic alignment procedure is presented, based on a simple model of the transmitter-receiver overlap. The lidar mounted at the Naples University is used to test this method. A centering precision of few microradians is obtained through dedicated software controlling a gimbal-mounted mirror. The automatic alignment procedure is then assessed. In particular, the correctness of the center and of its error is determined. Finally, the system is applied to the monitoring of tropospheric aerosols, leading to the continuous retrieval of profiles with fine spatiotemporal resolution.