Polymer bi-layer systems are often exposed to different environmental service conditions which can potentially alter the mechanical properties as it approaches the glass transition temperature of an inaccessible substrate. However, since the substrate is inaccessible, it is difficult to measure or quantify the changes in these properties while in use. A methodology has been proposed in this work for prediction of glass transition temperature and Young's modulus of an inaccessible substrate in a bilayer system. The composite mechanical property of a bi-layer system is a function of the mechanical properties of coating, substrate and the depth at which it is measured. In the present work, poly-Methylmethacrylate (PMMA) coating of ~900 nm is deposited on epoxy substrate. Nanoindentation experiments are conducted at different temperatures on the bi-layer system as well as on bulk PMMA. Finite element analysis has been used to obtain the material dependency of stress distribution coefficient (α) for deconvoluting the modulus of the substrate. The methodology developed by the present authors can predict the glass transition temperature as well the magnitudes of Young's modulus of an inaccessible substrate reasonably well.