Structural properties have been shown to be critical in the osteoconductive capacity and strength of bioactive ceramic bone scaffolds. Given the cellular foam-like structure of bone scaffolds, nanoindentation has been used as a technique to assess the mechanical properties of individual components of the scaffolds. Nevertheless, nanoindents placed on scaffolds may violate the rigid support assumption of the standard Oliver-Pharr method currently used in evaluating the Meyer hardness, H, and elastic modulus, Es, of such structures. Thus, the objective of this research was to use the structural compliance method to assess whether or not specimen-scale flexing may occur during nanoindentation of bioceramic bone scaffolds and to remove the associated artifact on the H and Es if it did occur. Scaffolds were fabricated using tricalcium phosphate and sintered at 950 °C and 1150 °C, and nanoindents were placed in three different (center, edge, and corner) scaffold locations. Using only the standard Oliver-Pharr analysis it was found that H and Es were significantly affected by both sintering temperature and nanoindents location (p<0.05). However, specimen-scale flexing occurred during nanoindentation in the 1150 °C corner location. After removing the effects of the flexing from the measurement using the structural compliance method, it was concluded that H and Es were affected only by the sintering temperature (p<0.05) irrespective of the nanoindent locations. These results show that specimen-scale flexing may occur during nanoindentation of components in porous bioceramic scaffolds or in similar structure biomaterials, and that the structural compliance method must be utilized to accurately assess H and Es of these components.