An understanding of the mechanical properties of viral capsids (protein assemblies forming shell containers) has become necessary as their perceived use as nano-materials for targeted drug delivery. In this thesis, a heterogeneous, spatially detailed model of the viral capsid is considered. This model takes into account the increased degrees of freedom between the capsomers (capsid sub-structures) and the interactions between them to better reflect their deformation properties. A spatially realistic finite element multi-domain decomposition of viral capsid shells is also generated from atomistic PDB (Protein Data Bank) information, and non-linear continuum elastic simulations are performed. These results are compared to homogeneous shell simulation re- sults to bring out the importance of non-homogenous material properties in determining the deformation of the capsid. Finally, multiscale methods in structural analysis are reviewed to study their potential application to the study of nanoindentation of viral capsids. / text