In this research, two major experiments, including the self-assembly of silica spheres, were performed by using a physical confinement method with an attractive capillary force. The silica spheres were dragged and aggregated as results of the evaporation of the solvent. In the first experiment, silica spheres were assembled into the two-dimensional pattered substrate, constructed by the photo-resist film formed under a lithography process. Several patterned substrates could work as a physical trap during the flow of the silica spheres. The ordered arrangement of the silica spheres was controlled by the concentration and the size of the silica spheres, the thickness of the photo-resist film, and the titled angle of the substrate. In our conditions, the silica spheres could orderly arrange in larger area of the substrate. In the second experiment, a surface-enhanced Raman scattering (SERS) enhancement was observed from a chain of silica spheres with silver nanoparticles, which worked as a excitation source to provid a strong local electromagnetic fields exciting the crystal violet (CV) dye coated on the silica spheres. We found that the CV molecules has a strong SERS intensity due to the refraction and reflection of the incident light within the silica spheres. When the silica spheres were linearly arranged, longer length of the chained silica spheres would lead to a maximum value of the SERS intensity.