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Nano-multi-layer (NML) ceramic thin films with the periodic (ITO/AlON)n and (ITO/SiOx)m structures were fabricated by the magnetron sputtering. The nano-size of film thickness was characterized by x-ray reflection (XRR) technique and field emission scanning electron microscopy (FE-SEM). The non-destructive XRR technique was able to analyze the NML films under sub-nano-meter-grade resolution quickly and precisely. From the XRR theoretical studies, two methods were used to simulate the characterization result in this study, the multiple-beam-interference (MBI) recursive method and the characteristic matrix method. Both methods show same calculation results. Finally, the periodic thickness and uniformity of NML thin films were compared by XRR and FE-SEM.