Nanotubular structures possess remarkable advantages in a broad range of areas, such as catalysis, sensing, microencapsulation, selective mass transport, filtration, and drug delivery. While the fields of carbon nanotubes and nanotubes made of several noncarbon materials (e.g., metals, oxides, semiconductors) have been progressing rapidly, proteinaceous nanotubes remained largely underexplored. Here, by retrofitting a template wetting approach with multiple silk-based suspensions, we present a rapidly scalable and robust technology for fabricating large arrays (e.g., 20 × 20 cm2) of well-aligned 1D nanostructures made of silk proteins. Benefiting from the polymorphic nature of silk, precise control over the size, density, aspect ratio, and morphology (tubes versus pillars) of silk nanostructures is achieved, which then allows for programmable modulation of the end materials' functions and properties (e.g., hydrophobicity, oleophilicity, and gas permeability). The silk nanotube arrays fabricated present great utility as antifouling coatings against marine algae and in oil extraction from oil-water mixtures.