The properties of the outermost surfaces of mesoporous silica thin films are critical in determining their functions. Obtaining information on the presence or absence of silica layers on the film surfaces and on the degree of mesopore opening is essential for applications of surface mesopores. In this study, the outermost surfaces of mesoporous silica thin films with 3-dimensional orthorhombic and 2-dimensional hexagonal structures were observed using ultralow voltage high resolution scanning electron microscopy (HR-SEM) with decelerating optics. SEM images of the surfaces before and after etching with NH4F were taken at various landing voltages. Comparing the images taken under different conditions indicated that the outermost surfaces of the nonetched mesoporous silica thin films are coated with a thin layer of silica. The images taken at an ultralow landing voltage (i.e., 80 V) showed that the presence or absence of surface silica layers depends on whether the film was etched with an aqueous solution of NH4F. The mesostructures of both the etched and nonetched films were visible in images taken at a conventional landing voltage (2 kV); hence, the ultralow landing voltage was more suitable for analyzing the outermost surfaces. The SEM observations provided detailed information about the surfaces of mesoporous silica thin films, such as the degree of pore opening and their homogeneities. AFM images of nonetched 2-dimensional hexagonal mesoporous silica thin films show that the shape of the silica layer on the surface of the films reflects the curvature of the top surface of the cylindrical mesochannels. SEM images taken at various landing voltages are discussed, with respect to the electron penetration range at each voltage. This study increases our understanding of the surfaces of mesoporous silica thin films, which may lead to potential applications utilizing the periodically arranged mesopores on these surfaces.