This article reviews the fundamental principles of the finite element method and the three basic steps (model creation, solution, and validation and interpretation) involved in using it to examine structural mechanics. Validation is a critical step in the analysis, without which researchers cannot evaluate the extent to which the model represents or is relevant to the real biological condition. We discuss the method's considerable potential as a tool to test biomechanical hypotheses, and major hurdles involved in doing so reliably, from the perspective of researchers interested in functional morphology and paleontology. We conclude with a case study to illustrate how researchers deal with many of the factors and assumptions involved in finite element analysis.