We present a site-specific elemental analysis of nano-scale patterns whereby the data acquisition is based on Rutherford backscattering spectrometry (RBS). The analysis builds on probing a large ensemble of identical nanostructures. This ensures that a very good limit of detection can be achieved. In addition, the analysis exploits the energy loss effects of the backscattered ions within the nanostructures to distinguish signals coming from different locations of the nanostructures. The spectrum deconvolution is based on ion-trajectory calculations. With this approach, we analyse the Ru area-selective deposition on SiO2-TiN line-space patterns with a linewidth of 35 nm and a pitch of 90 nm. We quantify the selectivity and the Ru local areal density on the top versus on the sidewall of the SiO2 lines. The sensitivity to probe ruthenium deposited on the various surfaces is as low as 1013 atoms/cm2. The analysis is quantitative, traceable, and highly accurate thanks to the intrinsic capabilities of RBS.