Although irradiation by an electron beam or nuclear reactor can result in creation of radioactive isotopes, this can be easily overcome by storing stones for a sufficient amount of time to allow residual radioactivity to decay.
Linac (linear accelerators) are the most common tool: higher E -> darker color (+ HEAT to remove brown tint). In the creation of "Sky blue" topaz, iradiation involves an electron beam with an energy below the activation threshold for all impurities except sodium (half life is about 15 hours). Thus, the small quantities of radioactive isotopes that form during electron irradiation decay away before the stones are released from the accelerator.