Biodiesel is growing in popularity as an alternative liquid fuel which is better for the environment than petroleum diesel.  A critical challenge for biodiesel is cold weather performance, due to a freezing point of soy-based biodiesel, for example, of around 0 °C.  This work presents the pilot scale design and operation of a two-step reaction process to efficiently fractionate the saturated and monounsaturated methyl esters from biodiesel using urea and methanol.  The process takes advantage of clathrates which form between urea molecules and guest alkane chains during cooling.  These clathrates precipitate from solution allowing the separation of long straight-chain methyl esters from branched or polyunsaturated methyl esters.  The pilot scale operation produces modified low-temp biodiesel with a freeze point of less than -45 °C and a saturated fraction methyl ester blend which can be used in a variety of applications.  Urea and methanol are recycled in the process and the system is being designed and tested to “drop-in” to an existing biodiesel plant. Simulations based on pilot plant results were programmed in SuperPro Designer v6.0 and used to model industrial scale urea fractionation and to analyze the economics of such an operation.  These results as well as process flow optimization and conditions will be presented.