Linearity is just an assumption we make to simplify the modeling--in general to describe any physics, we write very complicated, nonlinear differential equations. "Linearity" then comes from our efforts to simplify those complicated equations in order to create a workable engineering model. Every problem is nonlinear, it matters only the degree. We don't model everything with nonlinear kinematics and/or materials, because it would be too expensive. Therefore we try to run linear models whenever possible. However, the assumptions built into the linearity must be considered with ever model. You should incorporate testing of any relevant assumptions into your interpretation of the results. The answer to the question "what should I calculate to test those assumptions?" is a very complicated one. Consider a nice smooth structure, no cracks it. Say all you were interested in was testing a material for nonlinearities. You have to have some idea what the material's constitutive relation (or material curve, stress vs. strain) is before the analysis. You would generally complete the analysis, first assuming the material indeed behaved linearly. Now test the linearity assumption. A metal (nonlinearity in composites and polymers should evaluated differently) is assumed to be nonlinear with the maximum stress exceeds the yield stress (even the choice of stress is not constant. What stress? Some use von Mises stress, others use max. shear, it depends strongly on accepted industry practice). Say you like von Mises. If the von Mises stress anywhere exceed's the material's yield stress, then the material is considered to behave nonlinearly. Testing the assumption--now set up the material in your analysis so that it is elasto-plastic (elastic perfectly plastic, Ramberg Osgood, etc.). Run the analysis again, this time make sure it does the nonlinear material analysis (some FE software runs the linear analysis first, then the nonlinear analysis starts with this linear solution to complete the nonlinear analysis). Check the max. von Mises stress again--if the max. von Mises stress in this nonlinear run was less than one percent smaller than the von Mises stress calculated in the linear solution, then you can say the linear solution was adequate because the nonlinearities (in this case, plasticity) was small.