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We report on the controlled manipulation of two, three and four gold nanoparticles (AuNPs) using an atomic force microscope (AFM) for use as surface-enhanced Raman scattering substrates. For each arrangement, the interparticle electromagnetic (EM) coupling between adjacent AuNPs is studied at different polarization angles. It is found that the strength of EM coupling strongly depends on the arrangement of the AuNPs. In particular, the highest enhancement and the most pronounced polarization dependence is found for linear arrangement of closely spaced particles. Our results show that AFM manipulation has great potential for fabrication and investigation of controlled arrangements of nanoscale objects.