An optical discrimination technique, tailored to nanometric-sized, low optical absorbance molecular complexes adhering to thin metal films, is proposed and demonstrated. It is based on a time-resolved evanescent-wave detection scheme in conjunction with hierarchical cluster analysis and principal value decomposition. The present approach aims to differentiate among molecular films based on statistical methods, without using previous detailed knowledge of the physical mechanisms responsible for the detected signal. The technique is open to integration in lab-on-a-chip architectures and nanoscopy platforms for applications ranging from medical screening to material diagnostics.