Multilayers, which consist of periodic/aperiodic nanometer-scale stacks of two or more alternating materials, fill a gap between visible light optics and natural crystal by realizing high near-normal incidence reflectivity in extreme ultraviolet and soft X-ray regions and diffraction-limited focusing in hard X-ray region. Before fabricating a multilayer, it is essential to design a structure that realizes the required optical features. The optimization process uses merit functions that are defined by the design targets. In this chapter, the designs of two typical aperiodic multilayer structure, X-ray supermirror and EUV beam splitter, are introduced. Precision characterization of multilayer structures is the key process in multilayer sciences as well in order to improve fabricating process and determine optical properties in use. Searching a most suitable structure model to approaching real one by comparing experimental and simulated results is essentially an optimization problem. In this chapter, by fitting the X-ray grazing incidence reflectivity and diffuse scattering curves, the realistic multilayer structures are determined accurately.