Abstract The surface of multicellular organisms is covered with epithelial cells that provide a barrier to the external environment. As part of this barrier function, most epithelia produce apical extracellular matrices (aECMs). The generation of such chemical and physical barriers requires specialized deposition of macromolecules and is likely to involve a spatial and temporal coordination of biochemical activities at the apical surface. A challenging task is thus to characterize key proteins that underlie apical cell surface organization and correct aECM assembly. The Drosophila trachea provides an excellent system to study aECM formation, as they produce an ordered aECM, called the cuticle. The tracheal cuticle is unique by its presence of cuticular ridges, called taenidial folds, which prevent collapse of tracheal tubes while allowing them to expand and contract along their length. A gene called filzig encodes a transmembrane serine protease and is required for taenidial organization. The aim of this research was to further understand Filzig function through characterization of filzig mutants and Filzig protein expression. The results showed that Filzig is expressed in cuticle-producing epithelia as cuticle deposition begins. Moreover, Flz localized to the apical epithelial surface, as well as to the aECM. The apical Flz localization does not reflect the pattern of cuticle ridges, indicating that Flz-localization is not a determinant for taneidial patterning. Instead, Flz might act on extracellular targets that localize to the future taneidial folds. Alternatively, Filzig is involved in a cascade of self-organizing activity of cuticular components to form the regular taenidial folds.