Instrumented nanoindentation techniques have been widely used in characterizing mechanical behavior of materials in small length scales. For defect-free single crystals under nanoindentation, the onset of elastic-plastic transition is often shown by a sudden displacement burst in the measured load-displacement curve. It is believed to result from the homogeneous dislocation nucleation because the maximum shear stress at the pop-in load approaches the theoretical strength of the material and because statistical measurements agree with a thermally activated process of homogeneous dislocation nucleation. For single crystals with defects, the pop-in is believed to result from the sudden motion of pre-existing dislocations or heterogeneous dislocation nucleation. If the sample is prestrained before nanoindentation tests, a monotonic decrease of the measured pop-in load with respect to the increase of prestrain on Ni and Mo single crystals is observed. A similar trend is also observed that the pop-in load will gradually decrease if the size of indenter tip radius increases. This dissertation presents a systematic modeling endeavor of energetics and kinetics of defect initiation in the stressed volume at small scales. For homogeneous dislocation nucleation, an indentation Schmid factor is determined as the ratio of maximum resolved shear stress to the maximum contact pressure. The orientation-depended nanoindentation pop-in loads are predicted based on the indentation Schmid factor, theoretical strength of the material, indenter radius, and the effective indentation modulus. A good agreement has been reached when comparing the experimental data of nanoindentation tests on NiAl, Mo, and Ni, with different loading orientations to theoretical predictions. Statistical measurements generally confirm the thermal activation model of homogeneous dislocation nucleation, because the extracted dependence of activation energy on resolved shear stress is almost unique for all the indentation directions. For pop-in due to pre-existing defects, the pop-in load is predicted to be dependent on the defect density and the critical strength for heterogeneous dislocation nucleation. The cumulative probability of pop-in loads contains convoluted information from the homogenous dislocation nucleation, which is sensitive to temperature and loading rate, and heterogeneous dislocation nucleation due to the unstable change of existing defect network, which is sensitive to the initial defect distribution.