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Controlling the kinetic behaviors of molecularly thin lubricant is a key technology for designing head-disk interfaces (HDIs) of hard disk drives (HDDs). Direct visualization of molecularly thin lubricant films is useful in investigating kinetic properties such as replenishment or retention of thin lubricant films. To meet this demand, we demonstrated that the ellipsometric microscope can provide real-time visualization with a sub-nm thickness resolution. In this paper, we present a method of measuring the thickness of the lubricant film. In this method, the phase difference between the lights reflected from the film-covered and uncovered regions of the disk is obtained from the polarizer angles; then the thickness is calculated from the phase difference. We verified the feasibility of the method theoretically and experimentally. Measurement error of less than 0.2 nm was experimentally achieved for molecularly thin lubricants. This method provides real-time and quantitative imaging of molecularly thin lubricants and can provide useful information for designing HDIs for high-density HDDs.