Copolymers of (2-hydroxyethyl methacrylate) (HEMA) and methacrylamide monomers conjugated with amino acids were synthesized and crosslinked with ethylene glycol dimethacrylate. The resulting library of copolymers was mineralized in vitro using two distinct methods. In the first mineralization method, the copolymers were polymerized in the presence of a sub-micron hydroxyapatite (HA) suspension. In the second method, copolymers were mineralized with HA using a urea-mediated process. The mechanical properties of all of the copolymers, both mineralized and not, were determined using nanoindentation under both load and displacement control. A power law fit to the initial unloading curve was used to determine a reduced elastic modulus for each material. Between 30 and 300 indentations were performed on each material, and ANOVA analysis was run to determine the statistical significance of differences in modulus between samples. Using nanoindentation, the 22 different samples had reduced modulus values ranging from 840 MPa to 4.14 GPa. Aspartic acid-methacrylate (Asp-MA) copolymers were not distinguishable from the pHEMA control material. Polymerization in the presence of HA created a more uniform material than the urea method of mineralization. Several challenges and solutions encountered in the nanomechanical testing of soft, heterogeneous materials are discussed. These results demonstrate that with proper experimental design, the mechanical properties of tissue engineering scaffold materials based on polymer-ceramic composite materials can be determined using small samples and nanoindentation techniques.