In this study, the authors evaluated the effectiveness of using the nanometer depth sensitivity of differential confocal microscopy (DCM) to measure the surface profile of the two-dimensional (2D) photonic crystal structure. The depth of the micropore on the 2D hexagonal photonic crystal sample can be measured within 4.2 nm resolution. The surface profile of the 2D photonic crystal structure on the photoresist can be obtained by the nondestructive and noncontact DCM method, and the results were comparable to those from the commercial atomic force microscope method.