Clarification removes contaminants such as fine pulp, water and resins. The oil can be clarified by allowing it to sit undisturbed for a few days and then removing the upper layer. If the oil needs further clarification, it can be filtered. Finally, the oil can be heated to drive off traces of water and destroy any bacteria. Very clean oil is important in all uses, including plant oil biodiesel.

Degumming is a critically important process for oilseed processors who use their raw plant oil as vegetable oil fuel. These gums are similar to normal triglycerides; however, one gum chain is a phosphorus molecule. Most of the gums are hydratable with water, meaning that either a normal settling or a water wash followed by settling will get gums out. Some of the gums are non-hydratables, so the oil must be mixed with phosphoric or citric acid to cause the non-hydratable gums to swell up and come out of solution. The amount of non-hydratable gums formed, as well as the acid content of the oil, will often depend on the oil extraction temperature. Within a certain temperature range, lipases, the enzymes that consume fats and oils, are active during oil extraction. These lipases can cause the free fatty acid (FFA) content or the amount of non-hydratable gums to increase. Higher gum levels and FFA levels are not good for biodiesel production. Getting the non-hydratable gums out may or may not be critical, depending on the application. For instance, most of the hydratable gums will come out in the glycerin phase in biodiesel production, if the oil is destined for further refining to produce high quality B100 biodiesel.