An array of nano-scale protrusions, called the nipple array, is found on the body surface of various invertebrates, and this structure is believed to decrease light reflectance and water wettability on the surface in the terrestrial environment. However, its potential functions have not been well studied in aquatic environments. Clavelina spp. are colonial ascidians that have the nipple array on their integumentary matrix (i.e. tunic). We examined the physical properties on the surface of the tunic of C. cyclus and C. obesa, such as hardness, wettability and refractive indices, to evaluate the functional importance of this structure. The tunic cuticle of both species was covered with the nipple array, and the cuticle of C. cyclus was bent into folds forming parallel plications. The Clavelina tunic was very soft and had high bubble- and oil-repellency. The refractive-index deviation between the tunic and seawater was 0.07–0.095 for 589-nm light (D-line). Rigorous coupled wave analysis (RCWA) showed that the nipple array slightly reduced reflectance on the surface and the parallel plications reduced the reflectance still more. The nanoimprinted plates imitating the parallel plications have higher bubble repellency and lower reflectance than the flat plates. These findings support the functional importance of the plications as well as the nipple array.