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Estimation of soft error sensitivity is crucial in order to devise optimal mitigation solutions that can satisfy reliability requirements with reduced impact on area, performance, and power consumption. In particular, the estimation of Single Event Transient (SET) effects for complex systems that include a microprocessor is challenging, due to the huge potential number of different faults and effects that must be considered, and the delay-dependent nature of SET effects. In this paper, we propose a multilevel FPGA emulation-based fault injection approach for evaluation of SET effects called AMUSE (Autonomous MUltilevel emulation system for Soft Error evaluation). This approach integrates Gate level and Register-Transfer level models of the circuit under test in a FPGA and is able to switch to the appropriate model as needed during emulation. Fault injection is performed at the Gate level, which provides delay accuracy, while fault propagation across clock cycles is performed at the Register-Transfer level for higher performance. Experimental results demonstrate that AMUSE can emulate soft error effects for complex circuits including microprocessors and memories, considering the real delays of an ASIC technology, and support massive fault injection campaigns, in the order of tens of millions of faults within acceptable time.