We applied shear force microscopy, an analog to attractive-mode atomic force microscopy, and near-field scanning optical microscopy (NSOM) to the study of surface roughness and nanoscale morphology in polyelectrolyte self-assembled layers, Our data show that the surface roughness of multilayer films on glass grows linearly with the number of polyelectrolyte bilayers for the first 10 bilayers, and then asymptotes at a surface roughness of 4 nm. The surface of these films is characterized by bumps of 100-500 nm in diameter and 25-50 run tall. In addition, the size and density of the bumps for each bilayer are uncorrelated to the previous surface. This result is in sharp contrast to what is observed for other self-assembled layer structures, such as metal-phosphonate and Langmuir-Blodgett self-assembly, where the surface roughness linearly increases with the number of layers. Subsurface morphology in thin films was observed via fluorescence NSOM of a dye-doped polyelectrolyte film. The NSOM images show domains of higher and lower fluorescence intensity, which could be assigned to local changes in the film thickness, suggesting that the dye molecules are uniformly distributed within the film. We also show that both the initial and asymptotic surface roughness can be dramatically decreased if the bare glass surface is treated with a high charge-density polyelectrolyte, such as poly(ethyleneimine) (PEI), prior to the bilayer formation. Finally, we observed that if the initial substrate is rough, growth of the polyelectrolyte layers acts to smooth the surface until the equilibrium value is reached.