High power densities and the implications of high operating temperatures on the failure rates of components are key driving factors of temperature-aware computing. Computer architects and system software designers need to understand the thermal consequences of their proposals, and develop techniques to lower operating temperatures to reduce both transient and permanent component failures. Until recently, tools for understanding temperature ramifications of designs have been mainly restricted to industry for studying packaging and cooling mechanisms, with little access to such toolsets for academic researchers. Developing such tools is an arduous task since it usually requires cross-cutting areas of expertise spanning architecture, systems software, thermodynamics, and cooling systems. Recognizing the need for such tools, there has been recent work on modeling temperatures of processors at the micro-architectural level which can be easily understood and employed by computer architects for processor designs. However, there is a dearth of such tools in the academic/research community for undertaking architectural/systems studies beyond a processor - a server box, rack or even a machine room. This paper presents a detailed 3-dimensional Computational Fluid Dynamics based thermal modeling tool, called ThermoStat, for rack-mounted server systems. Using this tool, we model a 20 (each with dual Xeon processors) node rack-mounted server system, and validate it with over 30 temperature sensor measurements at different points in the servers/rack. We conduct several experiments with this tool to show how different load conditions affect the thermal profile, and also illustrate how this tool can help design dynamic thermal management techniques.