SRAM-based FPGA devices manufactured in FinFET technologies provide performances and characteristics suitable for avionics and aerospace applications. The estimation of error rate sensitivity to harsh environments is a major concern for enabling their usage on such application fields. In this paper, we propose a new estimation approach able to consider the radiation effects on the configuration memory and logic layer of FPGAs, providing a comprehensive Application Error Rate probability estimation. Experimental results provide a comparison between radiation test campaigns, which demonstrates the feasibility of the proposed solution.