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Perfluoropolyether lubricant films on magnetic disks were observed by means of atomic force microscopy (AFM) with a fluoride-coated probe. The lubricant films could be observed directly because the adhesion force was decreased by the anti-wetting effect of the fluoride coating on the probes. We compared the molecular conformation of Z-dol (Mw: 2000, 3000, 6000, 8000) with that of Z-tetraol. Thus, we found that the film coverage of a lubricant with high molecular weight exhibited varying (i.e., higher and lower) step heights of the lubricant film boundary. The Z-tetraol film exhibited higher coverage and the higher step height as compared to Z-dol2000. To further study the step height measured by means of atomic force microscopy, we compared the step height with the shoulder height of the spreading profiles of the films. The step heights were almost equal to the shoulder height. We observed the lubricant film after shearing by using contact scanning mode atomic force microscopy. The coverage of the sheared lubricant film increased higher than the initial coverage before shearing. Subsequently, the lubricant molecular conformation was varied due to the shearing, and the coverage was increased.