We apply well-characterized silver nanowire grating (Ag-NWG) plasmonic surfaces as a Raman surface spectroscopy tool, which is based on surface-enhanced Raman scattering (SERS), to study the surface conformation characteristics of amine terminated alkanethiol self-assembled monolayers (SAMs). The surface conformation has implications for amine group availability, which is important when SAMs are used as linking layers for the binding of secondary molecules. Two different alkanethiols with different alkane chain lengths, namely 2-aminoethanethiol (cysteamine, CEA) and 11-aminoundecanethiol (AUT), are investigated. It is shown that both alkanethiols bind to Ag surfaces forming corresponding Ag-thiolates, however surface conformations, which are related to the ordering of the SAM, are different for these two SAM systems. The degree of SAM ordering is assessed by quantifying the integrated intensity ratio of the trans to gauche nu(C-S) vibrational bands from single spectra measurements and from spatially averaged spectra. These vibrational modes occur at different vibrational frequencies depending on the conformation (trans versus gauche) of the neighboring carbon atom. We demonstrate that the CEA SAMs are less ordered than AUT SAMs; thus, the amine terminal group availability differs between both systems.