Probably the Baffle Planner module would be well suited for creating the thin model (New module: Baffle planner - for designing surface patches).
There are a number of ways to do the thickness measurement. What imaging modality you will use? What is the voxel size? What is the diameter of the eardrum? What is the average thickness of the eardrum? What accuracy do you need for measuring the thickness? What is the goal of determining the thickness (3D printing, surgical planning, quantification, …)?