A key thermal engineering challenge for integrating new nanostructured materials into devices is the development of accurate and reliable experimental and analytical techniques for thermal characterization across multiple length scales. We address this challenge by integrating the material synthesis with thermal property measurements and physics-based analysis. Often to achieve the desired functionality, multiples materials are combined together to form heterogeneous composites. For example, in lithium ion batteries, the particulate active materials (often with nanoscale features) are sandwiched between metal electrodes and polymer-based separators with microscale thicknesses to form macroscale battery cells. Here we develop an infrared thermography technique to probe the thermal transport properties and interface resistances in lithium ion battery cells. Ultimately the properties measured with microscale resolution can be incorporated into thermal-electrochemical models of the battery to predict performance and failure.