In recent years, three-dimensional IC (3D IC) has gained much attention as a promising approach to increase IC performance due to their several advantages in terms of integration density, power dissipation and achievable clock frequencies. However, the reliability of 3D ICs regarding soft errors induced by radiation is not investigated yet. In this work, we propose a method for evaluating the sensitivity of 3D ICs to Single Event Transient induced by Heavy Ions. The flow starts with identifying the characteristics of the generated transient pulses with respect to the radiation profile and 3D layout of the design. Secondly, our method provides a Dynamic Error Rate using a Simulation-based Fault Injection environment. Experimental results achieved applying the approach on a 15nm 3D configurable Look-Up-Table (LUT) designed on two tiers demonstrated the feasibility of the method, showing the vulnerability characterization of four different functional configurations using eight different types of heavy ions.