Computational models of the cell nucleus, along with experimental observations, can help in understanding the biomechanics of force-induced nuclear deformation and mechanisms of stress transition throughout the nucleus. Here, we develop a computational model for an isolated nucleus undergoing indentation, which includes separate components representing the nucleoplasm and the nuclear envelope. The nuclear envelope itself is composed of three separate layers: two thin elastic layers representing the inner and outer nuclear membranes and one thicker layer representing the nuclear lamina. The proposed model is capable of separating the structural role of major nuclear components in the force-induced biological response of the nucleus (and ultimately the cell). A systematic analysis is carried out to explore the role of major individual nuclear elements, namely inner and outer membranes, nuclear lamina, and nucleoplasm, as well as the loading and experimental factors such as indentation rate and probe angle, on the biomechanical response of an isolated nucleus in atomic force microscopy indentation experiment.