Gutting a fish is an important skill to learn, especially if you are into cooking. Unprocessed fish keeps better than the processed variety, so it is likely that you will encounter fish that has yet to be gutted. Taking out the gills and the intestines of the fish removes unwanted flavor in your dish, since these are the parts that tends to become very smelly or "fishy," when cooked. This is also the part where some of the undigested items are stored, so for hygienic purposes, it is best to take them out and throw them away.
Select a workstation that you do not mind getting dirty. The process of cleaning a flounder can splatter fish scales across the counter. Take out a sharp chef's knife, a chopping block and water, to help you rinse out the scales and insides later on.
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Remove the scales by running the knife at an angle against the grain of the fish. Do this in short, repetitive motions, to take out the scales. If you will be cleaning fish on your own often, invest in a scaling tool that looks like a zester. These run across the fish to loosen the scales. Rinse the fish in running water. Do this on both sides.
Insert your index finger between the fish's jaw and the gills to pry open its head. From here, you can see the deep red color of the gills. Scoop out the gills with your index finger and thumb. You can also cut the joint at the bottom of the jaw, so that you can easily take out the whole set of gills.
Locate the belly of the flounder, which is the underside of the fish, opposite its dorsal fins. With the tip of a sharp knife, run a single, deep incision across the belly, from the jaw all the way to the anus of the fish.
Pry this incision open and pull out the contents. These are the intestines and the liver, kidneys and other organs. Scrape out the lining of the belly carefully with a spoon, to remove stubborn innards.
Run the flounder under running water to get rid of excess scales, gills, blood and innards, before you put it back in the freezer for storage.