The surface of polyimide (PI) films for aligning liquid crystals were studied by means of atomic force microscopy (AFM). The surface of the unrubbed PI films consisted of polymer clusters of different sizes which are randomly distributed over the film area. After rubbing, however, these polymer clusters formed long chains along the rubbing direction. The cluster chains were separated with periodicity about 100 nm for weak rubbing strength. Deeper grooves are also present, separated with periodicity about 2 μm that could be related to the microstructure of the fibres from the rubbing cloth. On increasing the rubbing strength further on, the cluster chains coalesce into wider ones. The rubbed PI films show optical retardation, which was increased rapidly with increased the rubbing strength and reached a constant value of about 1.4nm.