We have developed a new method for characterizing paper coating structure using FIB milling technique and FE-SEM. A new image analysis method combining smart blur and locally adaptive thresholding technique was applied. Compared to conventional method, this method preserved the edge of target and gave better automatic image segmentation of pores. We applied this method for the measurement of the pore structure in pigment coating layers. Staining with OsO4 and resin-embedding treatments were used for the sample preparation of coated papers for image analysis. A control sample without any treatment was also used in analysis. BSE images of osmium stained and resin-embedded coated paper gave the clearest image segmentation of coating components. The results showed that three sample preparation methods gave similar z-directional porosities. Lower porosity and smaller pore size was obtained from the top surface layer with the osmium stained and resin embedded samples.