We present here a new approach based on high resolution scanning force microscopy that permits molecular determination and frictional discrimination between coexisting molecular configurations of alkanethiols on Au(111). The method has allowed visualizing in real time a phase transition between two differently ordered self-assembled configurations, which spontaneously takes place with time at constant coverage and under ambient conditions. Frictional force measurements indicate that the molecular rearrangement observed occurs via an order-disorder-order process.