Leather shoes are difficult to keep scratch-free, especially if you must use your fingers to buckle or tie them. Fingernail scratches may not be entirely removable, but you can reduce the look of them. Avoid future scratches by keeping your shoes well-conditioned with specialized leather moisturizers, lotions and creams.
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Dip a cotton swab in distilled white vinegar and dab it on the scratch. This will swell the scratched area slightly, so it doesn't look indented. Let it dry.
Buff the entire shoe with a leather conditioner, making small circles with a clean cloth. Avoid the scratched areas, as they may have a slightly different color or sheen than the rest of the shoe.
Color in the area with a cotton swab saturated in shoe polish if it is still too noticeable, or use a permanent marker in the same shade. Avoid non-permanent markers, or those that aren't waterproof, so you don't have color running.