We have characterized the binary LB films of merocyanine dye (MS) and arachidic acid (C20) before and after hydrothermal treatment (HTT), which is defined as a heat treatment under relative humidity of 100%, focusing on the morphology studied by bright field (BF) microscopy and fluorescence (FL) microscopy. BF microscopy observation has revealed that the as-deposited MS-C20 binary LB film is found to emit intense red fluorescence over the whole film area by 540-nm excitation. Since the surface image is almost featureless, it is considered that the crystallite sizes of J-aggregate are less than 10 μm. Interestingly, after HTT, round-shaped domains are observed in the LB systems, and the sizes are reaching 100 μm in diameter. Crystallites of J-aggregate, which are bluish in color and emit intense red fluorescence, tend to be in the round domains. We have observed two different types of domains, i.e., blue-rimmed domains and white-rimmed domains, which are postulated to be confined in the inner layers and located at the outermost layer, respectively. The thickness of the domains is equal to or less than that of the double layer of the MS-C20 mixed LB film, which is ca. 5.52 nm. The molecular order of MS in the J-aggregate is improved by the HTT process leading to the significant sharpening of the band shape together with the further red shift of the band (from 590 to 594 nm up to 597 to 599 nm). The reorganized J-band is considered to be ‘apparently’ isotropic owing to the random growth of the J-aggregate in the film plane. We consider that the lubrication effect by the presence of water molecules predominates in the HTT process.