In some metazoans, the body surface is entirely or partly covered with an array of nipples about 100 nm or less in height. This structure, a nipple array, is sometimes called the moth-eye structure because it serves as an anti-reflection property on the compound eyes of a night moth. The nipple array is supposed to be a multifunctional structure since this structure occurs in various species across different taxa. Here, we hypothesize that the nipple array may prevent the settlement of epibionts that are often a nuisance and potentially cause serious problems for the host. Using a synthetic film that imitates the nipple array, we tested the substrate selection within ascidian larval settlement. The results indicate that the nipple array has anti-fouling properties, since more larvae settled on the flat surface than the nipple array (P < 0.01, paired t-test). The present results demonstrated that the nipple array potentially serves an anti-fouling function on the body surface, which should be important especially for sessile organisms.