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Embedded systems can be engineered using clean room software engineering methodology (CRSE) as it considers all the quality issues as integral part of the CRSE life cycle model and lays stress on the reduced size and effort of testing through statistical use testing. Both CRSE and embedded systems development methodologies are based on stimulus-response models. The stimulus-response models are used for designing the external behavioral requirements. Thus, CRSE, in a revised form, can be conveniently be used for the development of reliable embedded systems. Verification and validation of one model with the other such as verifying the external behavior models (black box structures) with the requirement specifications and vice versa is the most important built-in feature of CRSE. In the literature the verification and validation methods described are manual step by step procedures which are either intuitive or experience based. CRSE suffers from lack of formal frameworks to verify box structures with the requirement specification and vice versa. In this paper, a methodology is proposed for verifying black box structures which are derived using end-to-end processing requirements of the embedded systems. The verification mechanism is built around generation of stimulus-response sequences in two different ways and proving that the sequences generated are the same when the system has been properly built. The stimulus-response sequences generation from the perspectives of thin threads and use case models has been presented in this paper.