The organization of thin films of symmetric poly(styrene-b-methyl methacrylate) diblock copolymers on silicon is investigated by neutron and X-ray reflectivity. The surface and internal structure as a function of annealing time is compared for two sets of films 680 and 800 Angstrom in thickness. For the thicker films the equilibrium morphology shows no surface features since the film thickness is 2.5L where L is the period of the lamellar microdomain morphology. The thinner films, 2.1L in thickness, exhibit hole formation over 40% of the surface. In both cases the multilayer organization proceeds from the substrate upward by chain transport through channels which perforate the developing layers. For short annealing times a sharp increase in surface roughness is seen, which may be linked with the wetting of PMMA-rich surface regions by polystyrene. At longer times these height fluctuations decay or grow into holes, depending on the initial film thickness.