We prepare various polymer-based microstructures for gold colloid detection in a Raman system. Several surface treatment techniques as well as chip configurations are discussed with an emphasis on their strengths and limitations. First, the optimum focus space is found for the experiment. Next, surface treatment effects for the Raman signal on the polymer-based substrate are compared. Finally, the Raman intensity of three channel configurations is compared along the cross sectional direction. There results demonstrate that a triangle shape provides the highest intensity for the same microstructure depth. A signal-enhanced mechanism on the difference cross sectional surface is also discussed in this research. Optimal shape designs based on polymer-based configurations are proposed for Raman detection in microchannels. This can give rise to several interesting applications, including trapping viruses from samples, and enzymatic reaction from enzymatic immuno-assay systems for real-time monitoring.