The fluorescent confocal scanning optical microscope is capable of 3-D observation, for which depth discrimination is vital. To characterize the depth discrimination capability of this microscope, intensity variations depending on fluorescence wavelength are simulated for fluorescent films being moved in the depth direction. Also, the resolution between two films is calculated for a range of fluorescence wavelengths. Results of experiments using photoresist films are compared to simulations. As a practical application, through-holes opened in a thick photoresist film are observed by slice images in the depth direction.