Simulations of nanoindentation in single crystals are performed using a finite temperature coupled atomistic/continuum discrete dislocation (CADD) method. This computational method for multiscale modeling of plasticity has the ability of treating dislocations as either atomistic or continuum entities within a single computational framework. The finite-temperature approach here inserts a Nose-Hoover thermostat to control the instantaneous fluctuations of temperature inside the atomistic region during the indentation process. The method of thermostatting the atomistic region has a significant role on mitigating the reflected waves from the atomistic/continuum boundary and preventing the region beneath the indenter from overheating. The method captures, at the same time, the atomistic mechanisms and the long-range dislocation effects without the computational cost of full atomistic simulations. The effects of several process variables are investigated, including system temperature and rate of indentation. Results and the deformation mechanisms that occur during a series of indentation simulations are discussed.