We demonstrate the suitability of two cost efficient technologies, namely roll-to-roll hot embossing and laser-assisted hot embossing, to fabricate arrays of structures in the microscale down to the sub-100 nm range. We therefore employ polymers with a relatively moderate glass transition temperature, e.g., cyclic olefin copolymer (COC) and polystyrene (PS). We compare the two replication processes regarding their precision and cost using different 1D and 2D nanostructure gratings and microfluidic channels. All nickel shims used for the replication are fabricated in combination of electron beam or UV lithography and nickel electroforming. The replicated structures are used in different applications. The nanopillar arrays are coated with gold and integrated in the hot embossed microfluidic channels for lab-on-a-chip (LoC) surface-enhanced Raman analysis. We evaluate the as-fabricated 2D nanopillar arrays for surface-enhanced Raman spectroscopy (SERS) using solutions of rhodamine 6G as exemplary analytes. The influence of the geometrical parameters like diameter and pitch of the polymer structures as well as the influence of the gold layer thickness are discussed. 1D-gratings will be used as resonators for organic distributed feedback (DFB) lasers. Both elements, the SERS chips and the organic DFB lasers as tunable excitation source can be combined in the future to form one Raman-on-Chip optofluidic platform for sensitive detection of low-concentrated analytes in water.