A method for forming a nanostructure penetrating a layer and the device made thereof is disclosed. In one aspect, the device has a substrate, a layer present thereon, and a nanostructure penetrating the layer. The nanostructure defines a nanoscale passageway through which a molecule to be analyzed can pass through. The nanostructure has, in cross-sectional view, a substantially triangular shape. This shape is particularly achieved by growth of an epitaxial layer having crystal facets defining tilted sidewalls of the nanostructure. It is highly suitably for use for optical characterization of molecular structure, particularly with surface plasmon enhanced transmission spectroscopy.