Sensors based on surface plasmons or waveguide modes are at the focus of interest for applications in biological or environmental chemistry. Waveguide-mode spectra of 1 μm-thick pure and perforated silica films comprising isolated nanometric holes with great aspect ratio were measured before and after adhesion of streptavidin at concentrations of 500 nM. The shift of the angular position for guided modes was nine times higher in perforated films than in bulk films. Capturing of streptavidin in the nanoholes is at the origin of that largely enhanced shift in the angular position as the amplitude of the guided mode in the waveguide perfectly overlaps with the perturbation caused by the molecules. Hence, the device allows for strongly confined modes and their strong perturbation to enable ultra-sensitive sensor applications.