The radiation-induced soft errors significantly increase the failure rate for advanced electronic components and systems. Rad-sensitive microprocessor-based devices working in the radiation environment are one of the most sensitive parts of the machine. This paper is focusing mainly on the strict software mitigation technique, called Software Implemented Hardware Fault Tolerance (SIHFT). SIHFT methods are based on the redundancy of variables or procedures implemented in compiled project. Sophisticated algorithms are used to check the correctness of control flow in the application. Several articles describe in details theoretical information about software protection algorithms but problem of efficient and error-proof implementation of these methods has always been omitted. Unfortunately, manual implementation of presented algorithms is difficult and can introduce additional problems with program functionality caused by human errors. Presented solution is based on the automatic implementation of SIHFT algorithms during the compilation process. Several modifications of software methods were proposed to make theoretical algorithms possible to the automatic installation.