Plasmonic properties of self-assembled silver nanoparticles/nanowires array on periodically patterned Si (100) substrate are reported with special attention on the mechanism of nanoparticles self-assembly. The advantage of this bottom up approach over other self-assembling and lithographic methods is the flexibility to tune array periodicity down to 20 nm with interparticle gaps as low as 5 nm along the ripple. Ripple pattern have shallow modulation (~2 nm) still particles self-assembly was observed in non-shadow deposition. Therefore adatoms diffusion and kinetics is important on ripple surface for the self-assembly. PVD e-beam evaporation method used for deposition has proven to be superior to sputter deposition due to lower incident flux and lower atom energy. It was found that particles self-assembly largely dependent on angle of incidence, substrate temperature, and deposition direction due to ripple asymmetric tilt. Ostwald ripening observed during annealing on ripples substrate has striking dependency on ripple periodicity and was found to be different compared to Ostwald ripening on flat Si surface. In-situ RBS measurements of deposited silver on flat and rippled substrate confirmed different sticking of atoms on the two surfaces. The difference between maximum and minimum of the calculated local flux show a peak at an incidence angle of 70o with respect to surface normal. This explains the best alignment of particles at this angle of incidence compare to others. Self-assembled nanoparticles are optically anisotropic, i.e. they exhibit a direction dependent shift in LSPR. The reason of the observed anisotropy is a direction dependent plasmonic coupling. Different in plane and out of the plane dielectric coefficients calculated by modelling Jones matrix elements, confirms that nanoparticle/nanowire array are biaxial anisotropic (ex ¹ ey ¹ ez). The nanoparticles are predominantly insulating while nanowires are both metallic and insulating depending on the dimension. Silver nanoparticles/nanowires self-aligned on pre-patterned rippled substrate are presented for the first time as an active SERS substrate. Anisotropic SERS response in such arrays is attributed to different field enhancement along and across the ripples. Strong plasmonic coupling in elongated nanoparticles chain results in significantly higher SERS intensity then spherical nanoparticles/nanowires and non-ordered nanoparticles. Higher SERS intensity across the nanowires array in comparison to along the array (bulk silver) confirms electromagnetic field enhancement (hot-junction) is responsible for SERS phenomenon. Self-assembly of cobalt nanoparticle on ripple pattern substrate is also reported. Due to less adatom mobility and higher sticking cobalt self-assembly is possible only at much higher temperature. A strong uniaxial magnetic anisotropy was observed not observed for non ordered cobalt particles.