The performance of devices based on organic semiconductors strongly depends on the molecular organisation in thin films. Due to the intrinsic complexity of these systems, a combination of theoretical modelling and experimental techniques is often the key to achieve a full understanding of their inner working. Here, we introduce the modelling of organic semiconductors by means of molecular dynamics simulations. We describe the basic theoretical framework of the technique and review the most popular class of force fields used to model organic materials, paying particular attention to the peculiarities of confined systems like nano-thick films. Representative studies of the organisation of organic functional materials in thin film phases are also reviewed.