We report grazing incidence x-ray scattering measurements made during in situ annealing of multilayers based on CoFe and CoFeB. The layer and interface structure of Co80Fe20/Ru multilayers grown on Si/ Al2O3 were found to be stable at all temperatures up to 400 ∘C. In contrast, Co64Fe16B20/Ru multilayers, also grown on Si/ Al2O3, showed loss of Kiessig fringe visibility above 270 ∘C but no evidence of Co64Fe16B20/Ru interface roughening on recrystallization of the Co64Fe16B20. We associate the changes in Kiessig fringe amplitude with increase in interface width, partly due to increase in the topological roughness, measured from the diffuse scattering away from the Bragg peaks, at the bottom Co64Fe16B20/ Al2O3 interface.