Analyses of molecule binding modes using SER fingerprints suggested that 4MPy and 4ABA assumed a roughly upright (4MPy) or horizontal (4ABA) position on the AuAg NPs. Furthermore, electric field simulation using FDTD suggested that excitation by TE or TM polarized light resulted in different electric field profiles on the AuAg NPs, with the TM mode showed greater attenuation compared to the TE mode.