Although bead microrheology experiments are routinely used to characterize the viscoelasticity of complex matter, their simulation analog—probe rheology molecular simulations—has been scarcely used since the system characteristics required for its robust implementation are not established in the literature. We address this issue by analyzing an active probe rheology simulation setup consisting of a probe particle that is subjected to an external oscillatory force and a harmonic trapping force. We identify a set of eight conditions of the system properties that must be satisfied for the successful implementation of the probe rheology technique in molecular simulations. Among these criteria, the two most important are as follows: (1) The spring force constant for the trapping force should be sufficiently large such that the peak in the Fourier transform of the probe displacement occurs at the same frequency as that of the applied force. (2) System parameters should be chosen such that the magnitude of the external force used to drive the probe motion should be comparable to the magnitude of the hydrodynamic friction force experienced by the probe particle in the viscoelastic medium. Furthermore, a scaling relation that can be used to determine the frequency at which inertial effects set in for a given probe size is also established. The validity of our procedure is demonstrated by applying it to determine the viscoelastic properties of a weakly entangled polymer melt system.