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Additive manufacturing (AM) is often used to create designs inspired by topology optimization and biological structures, yielding unique cross-sectional geometries spanning across scales. However, manufacturing defects intrinsic to AM can affect material properties, limiting the applicability of a uniform material model across diverse cross-sections. To examine this phenomenon, this paper explores the influence of specimen size and layer height on the compressive modulus of polycarbonate (PC) and thermoplastic polyurethane (TPU) specimens fabricated using fused filament fabrication (FFF). Micro-computed tomography imaging and compression testing were conducted on the printed samples. The results indicate that while variations in the modulus were statistically significant due to both layer height and size of the specimen in TPU, variations in PC were only statistically significant due to layer height. The highest elastic modulus was observed at a 0.2 mm layer height for both materials across different sizes. These findings offer valuable insights into design components for FFF, emphasizing the importance of considering mechanical property variations due to feature size, especially in TPU. Furthermore, locations with a higher probability of failure are recommended to be printed closer to the print bed, especially for TPU, because of the lower void volume fraction observed near the heated print bed.