This work represents the next step in the ongoing development of a system to noninvasively estimate blood perfusion using thermal methods. A combination thermocouple/thermopile sensor records heat flux and temperature measurements on the tissue of interest (in this case skin) for a given period of time. These data, in combination with other experimental parameters, are read into a computer program that compares them to a biothermal finite difference model of the system. The program uses an iterative process incorporating Gauss Minimization to adjust parameters in the biothermal model until the predicted system behavior satisfactorily approximates the real world data. The result is an estimation of blood perfusion in the tissue being measured, as well as an estimate of the thermal contact resistance between the probe and tissue. The system is tested on human forearms, canine legs during laparoscopic spay surgery, and on a canine medial saphenous fasciocutaneous free tissue flap model. Experimental measurements, especially those performed on the tissue flap model, show distinct correlation between blood perfusion and bioprobe output. This research demonstrates the accuracy of the biothermal model and the parameter estimation technique, as well as the usability of the system in a clinical setting. / Master of Science