Fused filament fabrication (FFF) is a commonly used method for producing three-dimensional scaffolds using synthetic, degradable polymers. However, there are several variables that must be considered when fabricating devices for clinical use, one of which is storage conditions after printing. While the academic community has examined the impact of FFF on mechanical and thermal properties, there has been less focus on how storage conditions would affect the surface texture of scaffolds. Our hypothesis was that the surface, thermal and physical properties of FFF scaffolds are significantly influenced by the storage conditions. We evaluated the surfaces of FFF poly (ε-caprolactone) (PCL) and poly (ε-caprolactone-co-p-dioxanone) (PCLDX) strands that were stored at 4 °C, 20 °C, and 37 °C for 28 days. We monitored surface texture, physical and thermal changes to understand the effect of storage on the strands. The implementation of scale-sensitive fractal analysis and feature parameters revealed that storage conditions at 37 °C increased the number of hills and dales, as well as the density of peaks and pits compared to 20 °C and 4 °C, for both materials. The feature roughness parameters for PCL had up to 90% higher values than those of PCLDX, which correlated with the physical and thermal properties of the materials. These differences may impact further surface-cell interaction, highlighting the need for further evaluation for faster clinical translation. Our findings emphasize the importance of considering storage conditions in the design and manufacture of FFF scaffolds and suggest that the use of feature roughness parameters could facilitate the optimization and tailoring the surface properties for specific applications. © 2023 The Authors