Nanoscale communication systems operating in Ter-ahertz (THz) band are anticipated to revolutionise the healthcaresystems of the future. Global wireless data traffic is undergoinga rapid growth. However, wireless systems, due to their broad-casting nature, are vulnerable to malicious security breaches. Inaddition, advances in quantum computing poses a risk to existingcrypto-based information security. It is of the utmost importanceto make the THz systems resilient to potential active and passiveattacks which may lead to devastating consequences, especiallywhen handling sensitive patient data in healthcare systems. Newstrategies are needed to analyse these malicious attacks and topropose viable countermeasures. In this manuscript, we presenta new authentication mechanism for nanoscale communicationsystems operating in THz band at the physical layer. We assessedan impersonation attack on a THz system. We propose usingpath loss as a fingerprint to conduct authentication via two-stephypothesis testing for a transmission device. We used hiddenMarkov Model (HMM) viterbi algorithm to enhance the outputof hypothesis testing. We also conducted transmitter identificationusing maximum likelihood and Gaussian mixture model (GMM)expectation maximization algorithms. Our simulations showedthat the error probabilities are a decreasing functions of SNR. At 10 dB with 0.2 false alarm, the detection probability was almostone. We further observed that HMM out-performs hypothesistesting at low SNR regime (10% increase in accuracy is recordedat SNR =5 dB) whereas the GMM is useful when groundtruths are noisy. Our work addresses major security gaps facedby communication system either through malicious breachesor quantum computing, enabling new applications of nanoscalesystems for Industry 4.0.