Fatty acids generated during Fat Splitting, or methyl esters from a transesterification process, are generally purified by distillation to separate the fatty acids into groups according to their chain lengths. Depending on the distribution of fatty acids or FAME and their intended uses, the distillation consists of a series of distillation columns that are designed to create specific cuts of fatty acids at a specific purity level. With such a wide range of boiling points for various fatty acids and the impurities (usually monoglycerides) in the feedstock, the process is usually tailored to remove a heavy cut (pitch) that contains very little fatty acid. The rest is often separated into a narrow range of fatty acids, but not so narrow as to only contain a single chain length. For example, a FAME produced from palm stearine may be separated into a high purity C:12 feedstock for MES applications and a high CFPP biodiesel product.

Processes to separate by chain length are relatively simple to model based on the boiling points of various components. In order to separate components by degree of saturation, alternate methods of separation are often used because the degree of saturation does not change the boiling point of a fatty acid of a given chain length enough to be practical to separate by standard distillation. This is not to say it cannot be done, but only that the purity desired would likely create a distillation system too large to be economical.

During the process the components are sensitive to thermal degradation, so care is used to limit the amount of time spent at high temperatures. The distillation is done under vacuum to achieve a reasonable boiling point for the fatty acid cuts. An antioxidant can also be added to the finished product.