Molten Salt Reactors (MSRs) are an example of an advanced reactor designs that differ substantially from the existing commercial technology. Because the safety assessment of such reactor designs will require consideration of hazards that are not present in light water reactors (LWRs), a flexible method is needed to comprehensively identify and analyze new hazards and event sequences. This work demonstrates the application of a specific Process Hazards Analysis (PHA) methodology to select auxiliary systems of the Molten Salt Reactor Experiment (MSRE) design in order to provide safety insights to the design of these subsystems, as well as produce results that can be carried forward into more quantitative risk assessment approaches. Additionally, ongoing work to develop an MSR-specific component reliability database to support quantitative risk assessment is also described.