A methodology using magnetic resonance angiography (MRA) is presented for identifying thermally significant blood vessels in isolated kidneys, specifically for use in biothermal model development with application to high intensity focused ultrasound (HIFU). A combination of a proven preservation technique, newly developed MR-compatible experimental procedures and the refinement of MR pulse sequence parameters was used to determine vascular characteristics using high-resolution three-dimensional time-of-flight MRA image of flow through isolated kidneys. Results presented are twofold. First, improved vessel visibility was attained through decreasing the magnetic resonance imaging bandwidth from 150 to 30 Hz/pixel while simultaneously increasing the echo time, repetition time, and flip angle; vascular center line extraction showed an 18% improvement in the number of vessel segments detected and a 23% increase in length of the terminal segments over a base line technique without improvements. Second, the overall system was shown to be practical to determine vascular flow effects during HIFU heating; testing results from heating the kidney with HIFU are presented, showing a decrease of average kidney temperature with an increase of flow rate through the kidney with localized cooling demonstrated surrounding known vessel locations.