Abstract: The fabrication of nanoscale materials with porous anodic alumina (PAA) is an important research topic,for which it is necessary to measure the topography of PAA with high accuracy. The influence of gold plating on samples and the measuried scanning electron microscopy results are presented. Then, the method to measure PAA nondestructively by atomic force microscopy is investigated. The various results under different measuring modes are compared, and the influence of the "tip-surface convolution" on the results is revised. The significance of this research is not only in the porous anodic alumia research field but also in the measurement of nanoscale porous materials.