Layer-by-layer (LBL) films of a semiconducting polymer (POMA) alternated with a polyelectrolyte (PVS), adsorbed onto silicon oxide, mica, ITO/glass, Au/Cr/glass, hydrophilic and hydrophobic glass were studied by atomic force microscopy (AFM). The samples were characterized LBL with the AFM operating in the contact, friction and tapping modes, which allowed us to determine their morphological surface properties such as roughness, mean grain size, grain boundaries and power spectrum density. Their film thickness was measured by AFM using the tip as a scraping tool. Surface roughness increases with the number of bilayers until a constant value is reached. This is in agreement with the observed increase in the adsorbed amount (per layer) of POMA as the number of bilayers is increased, which also saturates after several bilayers. It is shown that the 3D growth behaviour indicates a similar microscopic mechanism for all systems under study, pointing to a stochastic growth process of the Eden model type, but strongly influenced by initial roughness and water affinity of the virgin substrates. The crystalline or amorphous nature of the substrates does not seem to influence the growth process.