Information from the Internet of Medical Things (IoMT) domain demands building safeguards against illegitimate access and identification. Existing user identification schemes suffer from challenges in detecting impersonation attacks which leave systems vulnerable and susceptible to misuse. Significant advancement has been achieved in the domain of biometrics and health informatics. This can take a step ahead with the usage of multimodal biometrics for the identification of healthcare system users. With this aim, the proposed work explores the fingerprint and iris modality to develop a multimodal biometric data identification and access control system for the healthcare ecosystem. In the proposed approach, minutiae-based fingerprint features and a combination of local and global iris features are considered for identification. Further, an index space based on the dimension of the feature vector is created, which gives a 1-D embedding of the high-dimensional feature set. Next, to minimize the impact of false rejection, the approach considers the possible deviation in each element of the feature vector and then stores the data in possible locations using the predefined threshold. Besides, to reduce the false acceptance rate, linking of the modalities has been done for every individual data. The modality linking thus helps in carrying out an efficient search of the queried data, thereby minimizing the false acceptance and rejection rate. Experiments on a chimeric iris and fingerprint bimodal database resulted in an average of 95% reduction in the search space at a hit rate of 98%. The results suggest that the proposed indexing scheme has the potential to substantially reduce the response time without compromising the accuracy of identification.