Multifunctional silica nanotubes (SNTs) are being widely used for many biomedical applications due to their structural benefits. Controlling the structure of the open end of an SNT is a crucial step for drug/gene delivery and for fabrication of multifunctional SNTs. We developed a mechanical capsulation method to fabricate caps at the ends of SNTs. A thin layer of malleable capping materials (Au, Ag, PLGA) was deposited onto the surface of an SNT-grown AAO template. Capped SNTs were then obtained by hammering with alumina microbeads. For a proof-of-concept experiment, we demonstrated dye-encapsulated SNTs without any chemical functionatizations. Since a mechanical approach is free of the issue of chemical compatibility between cargo molecules and capping materials, the method can provide an effective platform for the preparation of smart multifunctional nanotubes for biomedical applications.