Atomic Force Microscopy (AFM) and related techniques are used to investigate the morphology of diblock copolymers. We focus on compounds containing a conjugated segment, polyparaphenylene, associated to a polymethylmethacrylate or a polystyrene block. The influence of the presence of the conjugated segment on the microdomain morphology is analyzed as a function of chain composition. Separate microdomains are observed on the surface of thin films by means of phase-detection imaging tapping-mode AFM. Their shape and size are interpreted in terms of molecular aggregation, with the help of molecular dynamics calculations.