In this paper, a high order compact difference scheme has been developed for second order wave equations with piecewise discontinuous coefficients. The idea presented here can be used to solve a wide variety of hyperbolic models for nonhomogenous inner structures. Thermal wave model of bio-heat transfer in a multilayered skin structure with different thermal and physical properties is investigated subject to constant, linear, exponential and sinusoidal heating. The success of the new procedure is demonstrated by solving test problem as well as by application to the triple layered skin structure.