We demonstrate gold coated surface enhanced Raman scattering (SERS) substrates with a pair of complementary structures-positive and inverted pyramids array structures fabricated by polymer replication of each other. The SERS enhancement factors were measured uniformly as 7.2×104 for positive pyramids substrate while 1.6×106 for inverted pyramids substrate with Rhodamine 6G as the target analyte. Based on optical reflection measurement and finite difference time domain (FDTD) simulation result, we propose the explanation for the enhancement factor difference. It is attributed to plasmon resonance matching. With this simple, fast and versatile complementary molding process, we can produce SERS substrates with extremely low cost and high throughput.