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Reconstructing system-level behavior from silicon traces is a critical problem in post-silicon validation of System-on-Chip designs. Current industrial practice in this area is primarily manual, depending on collaborative insights of the architects, designers, and validators. This paper presents a trace analysis approach that exploits architectural models of the system-level protocols to reconstruct design behavior from partially observed silicon traces in the presence of ambiguous and noisy data. The output of the approach is a set of all potential interpretations of a system's internal executions abstracted to the system-level protocols. To support the trace analysis approach, a companion trace signal selection framework guided by system-level protocols is also presented, and its impacts on the complexity and accuracy of the analysis approach are discussed. That approach and the framework have been evaluated on a multi-core system-on-chip prototype that implements a set of common industrial system-level protocols.