We use the nonstandard-finite-difference time-domain (NS-FDTD) method to investigate the interaction of light with the complicated microstructures in the Morpho butterfly scales, which produce the well-known brilliant blue coloring. The NS-FDTD algorithm is particularly suitable to analyze such complex structures because the calculation can be performed in a short time with high accuracy on a relatively coarse numerical grid. We analyze (1) the microstructure obtained directly by binarizing an electron microgram of the cross section of a scale, (2) the reflection and diffraction properties of three model structures--flat, alternating, and tree-shaped alternating multilayers, and (3) an array of alternating multilayers with random noise superposed on the height of the structures. We found that the actual microstructure well reproduced the reflection spectrum in a blue region by integrating the reflection intensities over all the reflection angles. Under normal incidence, the flat multilayer mainly stresses on multilayer interference except for shorter wavelengths, while alternating multilayer rather enhances the effect of diffraction grating due to longitudinally repeating structure by strongly suppressing the reflection toward the normal direction. In the array of alternating multilayers, the reflection into larger angles is considerably suppressed and the spectral shape becomes different from that expected for a single alternating multilayer. This suppression mainly comes from the scattering of reflected light by adjacent structures, which is particularly prominent for the TM mode. Thus a clear difference between the TE and TM modes is observed with respect to the origin of spectral shape, though the obtained spectra are similar to each other. Finally, the polarization dependence of the reflection and the importance of the alternating multilayer are discussed.