We report Raman analysis of few-layer graphene (FLG) transferred on flat and patterned substrate structures. These different surface structures created by patterning an area of a Si-substrate produce differences in the interaction between FLG and the substrate surface. The topography measurement performed by scanning tunneling potentiometry shows that the FLG on the patterned substrate was deformed periodically with 3–4 nm depth variation. Raman spectroscopy reveals that two important features related to the G- and 2D-modes in graphitic structures show different sensitivity to the interaction with the substrate for single-layer graphene (SLG), FLG, and graphite. Whereas SLG and FLG placed on the patterned substrate demonstrate a strong shift of both 2D- and G-peaks to lower frequencies with respect to the flat part, the multilayer graphene in a graphite flake shows almost no difference between patterned and non-patterned substrates. We identified the origin of the observed changes in the Raman spectra of SLG and FLG as effects created by the underlying substrate. Especially, substrate induced periodic strain and surface interaction were taken into account to interpret the results.