Atomistic-based multiscale and molecular dynamics modeling are powerful tools to simulate the localized strain problems, offering tremendous opportunities to bridge the knowledge gaps in quantifying and understanding the linkage of plasticity mechanisms and nanomechanical/tribological response of materials at finite temperatures. In this article, we give an overview of these atomistic-based modeling techniques which are amenable to the nanoindentation/scratching at finite temperatures, and briefly describe the pertaining physics, e.g., long range dislocation motion and heat transfer, during nanoindentation/scratching at finite temperatures. We summarize the effects of temperature, loading rate, and crystallographic planes on the process of defect formation and migration as well as the nanomechanical/tribological response of a wide range of crystalline and amorphous materials subject to nanoindentation/scratching. Our review presents unresolved issues and outstanding challenges in atomistic-based modeling of nanoindentation/scratching at finite temperatures and sheds light on the path forward in this emerging research area.