The soft x-ray reflectivity of multilayer films is affected by the surface roughness on the transverse nanometer scale. Scanning tunneling microscopy (STM) is an ideal instrument for providing high-lateral-resolution roughness measurements for soft x-ray multilayer films that cannot be obtained with other types of instruments on the transverse nanometer scale. The surface roughnesses of Mo/Si, Mo/C, and W/Si soft x-ray multilayer films prepared by an ion-beam-sputtering technique were measured with a STM on the vertical and transverse attributes. The film roughnesses and average spatial wavelengths added to the substrates depend on the multilayer film fabrication conditions, i.e., material combinations, number of layers, and individual layer thickness. These were estimated to lead to a loss of specular reflectivity and variations of the soft x-ray scattering angle distribution. This method points the way to further studies of soft x-ray multilayer film functional properties and can be used as basic guidance for selecting the best coating conditions in the fabrications of soft x-ray multilayer films.