Multi layered systems are frequently used for thermal management where the quality of the layers and the interfaces are critical in achieving desired operating conditions. Defects that introduce an additional thermal resistance in the thermal path must be prevented. Non-destructive characterization tools such as computerized tomography or scanning acoustic microscopy have been used to identify such problems, and help improve manufacturing process to ensure product quality. In a system with opaque solids, thermal tomography that relies on a thermal signal diffusing through the layers can be used to identify the defects in the system. Such a technique can constitute a practical and low cost alternative to the other non-destructive testing methods necessitating expansive equipment. Feasibility of thermal tomography for characterization of multilayer systems is tested considering different measurement configurations based on areal and discrete measurements. The configurations are compared considering different geometric parameters with Levenberg-Marquard method used for image reconstruction.