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Bacteria biofilms in chronically infected wounds significantly increase the burden of healthcare costs and resources for patients and clinics. Because biofilms are such an effective barrier to standard antibiotic treatment, new methods of therapy need to be developed to combat these infections. Our group has demonstrated the potential of using Laser Generated Shockwaves as a potential therapy to mechanically disrupt the bacterial biofilms covering the wound. Previous studies have used rigid silica glass as the shockwave propagation medium, which is not compatible with the intended clinical application. This paper describes the exploration of five candidate flexible plastic films to replace the glass substrate. Each material measured 0.254 mm thick and was used to generate shockwaves of varying intensities. Shockwave characterization was performed using a high-speed Michelson displacement interferometer and peak stress values obtained in the flexible substrates were compared to glass using one-way nested Analysis of Variance and Tukey HSD post-hoc analysis. Results demonstrate statistically significant differences between substrate material and indicate that polycarbonate achieves the highest peak stress for a given laser fluence suggesting that it is optimal for clinical applications.