An analytical approach using enhanced Raman spectroscopy to record molecular vibrations and associated molecular images within nanometric apertures is presented, which can essentially rival or surpass its counterparts, i.e. fluorescence microscopy, by providing unique structure-specific information forward to chemical identification and structure elucidation. Utilizing a precise nanolithographic technology and the following chemically electroless silver deposition procedure, we deliberately construct the large scale zero-mode waveguide array in gold film with embossed silver nanostructures on the bottom of nanowells capable of acquiring enhanced Raman spectra with substantial sensitivity and high chemical fidelity. Two chemicals, aminothiophenol (4-ATP) and Rhodamine 6G, respectively, are employed as molecular indicators to successfully demonstrate the capability of this analytical strategy by exhibiting high-quality Raman spectra and 2D chemical-specific images. With a high magnitude objective (60×), we enable to acquire Raman spectra from a single nanometric aperture and quantitatively determine a peak enhancement factor of 3.63 × 105 for ATP, while 1.25 × 106 to Rhodamine 6G, comparable with a regular nanoparticle-based surface-enhanced Raman spectroscopy-active substrate. Overall, the compelling characteristics of this detection scheme highlight its privileges for interrogating the individual molecular behavior in extremely confined geometry and illustrating the chemical insights of trace components without any labeling reagent and extra sample preparation. Copyright © 2013 John Wiley & Sons, Ltd.