I will report on measurements of the elastic properties of two types of 2D-crystalline shells, microtubules and bacteriophage capsids, probed by indentation with a scanning force microscope (SFM). Both, microtubules and viral capsids are protein shells and we found a linear elastic regime that can be described by thin-shell theory and finite element methods. We also found a non-linear regime and catastrophic collapse under large loads. The mechanical response of these protein shells at the nanometer scale shows simultaneously aspects of continuum elasticity, as well as molecular graininess, particularly in their non-linear behavior.