Ultrathin nanofilms of siloxane derived from methyltrichlorosilane (MTCS) and 3-aminopropyltrimethoxysilane (APTMS) were formed on the surface of silicate glass and investigated using infrared specular reflectance (IR-SR) spectroscopy. To differentiate the spectral bands of the film from those of the glass substrate, two-trace two-dimensional correlation spectroscopy (2T2D-COS) was employed. The spectra analyzed were either IR-SR spectra of unmodified and surface-modified glass or reflectance-absorbance (RA) spectra, calculated from ratio-reflectance (RR) spectra. The spectral region studied focused on the Si-O-Si stretching and bending vibrations, corresponding to the absorption-reflection IR region of the glass. The results demonstrated that 2T2D-COS enables the distinction of bands attributed to the film, not only for nanofilms with a thickness of approximately 80 nm but also for ultrathin nanofilms ranging from 3 to 10 nm. Additionally, specific characteristics of the 2T2D-COS spectra derived from the IR-SR spectra were discussed, along with precautions considered which are necessary to avoid mistakenly attributing glass bands to the film.