In this study, we prepared large-area polydimethylsiloxane (PDMS) 3D flexible films deposited with silver nanoparticles (Ag NPs) by assembling Ag NPs on ordered micron-column (MC) arrays fabricated using SU-8 colloidal lithography (Ag NP@SU-8-MC). The large-scale, highly ordered 3D MC array flexible film offers numerous adsorption sites for densely packed Ag NPs. High-density sub-nanometer gaps between Ag NPs create spatial hot spots, enhancing the electromagnetic field. The results indicate that this flexible substrate achieves a detection limit of 10-15 M for rhodamine 6G (R6G), with a relative standard deviation of less than 8 %, demonstrating excellent SERS sensitivity and uniformity. Furthermore, leveraging its high viscosity and flexibility, the 'pasting-extraction' method was employed to detect carbendazim and thiram on the surfaces of tomatoes and apples, achieving detection limits of 10-10 M and 10-11 M, respectively. Overall, this work presents a practical approach for preparing flexible and sensitive SERS substrates for food safety applications.