A separatory funnel's stopper is located on the top of the flask. You must remove the stopper to add the solution you wish to extract a solute from. After the extraction takes place, you must remove the stopper a second time to pour out the remaining solute and clean the funnel. Although the stopcock has a small opening, it works as a tap. You can drain liquids out thorough the stopcock, but you must use the stopper opening when pouring liquids into the funnel.
Separatory funnels date back to the turn of the 20th century. For most of its history, a separatory funnel had as standard equipment a ground glass stopper. That is no longer the case. Plastic stoppers are an alternative to glass in modern separatory funnels. While ground glass stoppers are effective, they have certain disadvantages. Not only are ground glass stoppers breakable, but if you forget to remove a glass stopper after working with the separatory funnel, the stopper can lodge permanently in the funnel's opening – rendering the funnel useless. Plastic stoppers, on the other hand, don't lodge permanently in the funnel, and a plastic stopper won't break if you accidentally drop it.
You already know that you must remove the separatory funnel's stopper when putting liquid into or draining liquid out of the funnel's main opening. You must also remove the stopper when extracting liquid from the funnel using the stopcock.
Pressing down on the stopcock releases trapped gas and prevents the pressure from building too high within the funnel. It also drains the separated solute after extraction. When using the stopcock to drain a separated solute, you must remove the top stopper as well. This prevents a vacuum from building. Should a vacuum occur, the extracted solute will not drain.
It's crucial that the stopper on your separatory flask is watertight. A loose stopper could result in dangerous leaks of caustic chemicals, not to mention failed experiments. If your ground glass stopper does not properly seal off the funnel, apply a small amount of grease to the upper part of the funnel's opening. The grease helps the stopper adhere better – allowing you to continue with your work.