The pop-in effect in nanoindentation of metals represents a major collective dislocation phenome-non that displays sensitivity in the local surface microstructure and residual stresses. To under-stand the deformation mechanisms behind pop-ins in metals, large scale molecular dynamics simulations are carried out to investigate the pop-in behavior and indentation size effect in unde-formed and deformed Cu single crystals. Tensile loading, unloading and reloading simulations are performed to create a series of samples subjected to a broad range of tensile strains with/without pre-existing dislocations. The subsequent nanoindentation simulations are con-ducted to study the coupled effects of pre-strain, the presence of resulting dislocations and surface morphology, as well as indenter size effects on the mechanical response in indentation processes. Our work provides detailed insights into the deformation mechanisms and microstruc-ture-property relationships of nanoindentation in the presence of residual stresses and strains.