A three dimensional thermal imaging system is being developed for measuring temperature profiles in MEMS-biomedical devices. These devices rely on a thermal microablation of the dead-skin layer in order to sample transdermal fluids. This is accomplished using microheaters embedded into a PDMS microchannel device. In order to determine the proper functioning as well as long-term safety of the devices, a temperature profile of the device and the skin in contact with the heaters is needed. The results of simple analytical models are used to optimize a proto- type device. Using a three-dimensional chemical imaging microscope and temperature-depend- ent fluorophores, the temperature profile in a sample can be determined quantitatively as well. We demonstrate the technique on a model sample, and discuss extension to other applications such as thermal imaging in biological systems.