Fault tolerance techniques implemented at software level have been widely studied as an approach to improve reliability in processor-based systems. This paper presents a fault injection software-based methodology to emulate soft errors in processors running operational systems. The proposed method aims to accelerate the analysis of complex systems under soft errors in order to assist the development of fault tolerance mechanisms. In order to validate the proposed methodology, a simulator was implemented based on QEMU software. QEMU emulates a large number of well-known microprocessor architectures with a full system composed by memory and I/O devices. A case-study for an operational system - the Real Time Operating System (RTEMS) - running in X86 architecture was designed in the QEMU platform and faults were injected. Results show the susceptibility of the registers to faults and can guide designers in the fault tolerance techniques implemented at software level.