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You get fingerprints because of ridges in your fingers. Henna is just a paint/dye and your fingerprints don't get affected by it . But henna is not universally known and immigration officers from other countries may suspect it. There have been incidents where immigration officers did not consider your fingerprints with henna. It is safe if you don't apply henna if you are flying to other country. Or best of both worlds, you apply henna on rest of your hand keeping your fingers clean.