An experimental study was conducted to classify the influence of trabecular architecture and cortical shell thickness on the mechanical properties using a bone surrogate. Thirty-six rectangular prisms and 18 vertebral-shaped specimens were fabricated with fused deposition modelling (FDM) as a bone surrogate with controlled structural characteristics (cortical wall thickness, strut spacing, strut angle and strut orientation). The apparent density of the FDM specimens was evaluated using quantitative computed tomography (QCT) imaging and related to the apparent elastic modulus measured with compression testing. The effects of the structural parameters on the apparent elastic modulus were analysed using analysis of variance (ANOVA). The results obtained corroborate that the structural parameters have a significant effect on the apparent mechanical properties of the bulk material. The cortical shell thickness was found to have more influence than trabecular architecture. Therefore, accurate modelling of the cortical shell thickness should be considered more important than trabecular architecture in development of bone finite element models and bone surrogates.