Ideal descriptors of hyperthermia treatments will most likely depend on complete target temperature distributions. Although these distributions can be modeled numerically, the accuracy of models is limited by the sparseness of temperatures measured in vivo. Thus, the strategy of monitoring temperatures may play a key role in improving hyperthermia therapy. Scanning temperatures by manual translations of thermometers was found to be excessively time consuming. Consequently an automated system was developed consisting of linear actuators, outriggers, guide tubes, thermometry catheters, personal computer, and dedicated hardware and software. During treatments, scan patterns were created with algorithms using temperatures measured preceding each thermometer translation. Measurement position had a noteworthy influence on thermal dose estimated by current models. Relative to manual scanning, automated scanning increased measurement efficiency, reduced probe position uncertainty, reduced operator time, and provided improved data for modeling bioheat transfer and thermal dose.