"If your nose runs and your feet smell, you're built upside down." Meathead
The bane of all bakers is a runny, soupy pie. When you cut into it, the filling runs into the pan and the pie deflates. So experienced bakers use some sort of a thickener to make it nice and firm. The amount of thickener depends on the liquid and the amount of pectin, a natural thickener in the fruit. It is a bigger problem with some fruits than others, especially apple, strawberry, blackberry, raspberry, peach, plum, and nectarines. Cherries and blueberries are less juicy while apples have more natural pectin than berries. Riper fruits are softer and juicier than slightly underripe fruits.
Flour: Not recommended
Many older home bakers use all purpose flour. Flour can make the filling cloudy, can have a starchy taste, and a gritty texture. It is not recommended. If a recipe calls for all-purpose flour, experts say to substitute one of the below options.
Corn starch is better because it sets clear, but it can be a bit gummy and it can break down and become watery under the heat of baking. For a 9" apple pie, try 2 tablespoons of cornstarch. More for juicier fruits such as berries and stone fruit.
Instant tapioca: Better still
A lot of bakers recommend tapioca, a starch from cassava or manioc root. Among those, tapioca seems to be the fave because it has great absorbing power, it is practically invisible, adds gloss, is clean tasting, and it doesn't break down in acidic fillings, or when frozen, or under high heat as some of the other thickeners do. Tapioca can be stored indefinitely in a cool dry place. It is available in four forms:
1) Tapioca flour, tapioca starch, cassava flour is a powder that some bakers prefer to instant tapioca for pies. For a 9" apple pie, try 2 tablespoons of instant tapioca. More for juicier fruits such as berries and stone fruits.
2) Instant tapioca is also called quick tapioca, quick cooking tapioca, tapioca granules, and instant pearl tapioca are great for pies. Minute Tapioca is the brand name for instant tapioca owned by Kraft. Instant tapioca is granulated and this is the stuff used for thickening pie fillings, stews, gravies, and soups. Because it doesn't dissolve completely and it can leave small gelatinous blobs you should pulverize it in a food processor, blender, spice grinder, coffee mill, or mortar and pestle. This form takes a little time to "bloom" and do its magic, so it needs to be added to the filling at least an hour before baking.
3) Large beads, pearl tapioca beads, tapioca balls, or fisheye tapioca are BB sized pellets, and they are used to make tapioca pudding or "bubble" drinks now gaining in popularity in Asian restaurants. They don't dissolve entirely and make squishy, gelatinous balls. Don't use these in a pie.
4) Regular tapioca, small bead tapioca, or small pearl tapioca, are also used in pudding, but are too large and don't dissolve completely, so they're not recommended for thickening pie filling.
Many commercial bakers and expert home bakers use a product called Instant ClearJel, a modified food starch known to remain clear and keep its thickening power under both hot and cold conditions. It can even be used to thicken fresh berry pies that are not baked. Use slightly less than flour, and slightly less than double the amount of corn starch or tapioca, but the right amount depends a lot on the fruit, its ripeness, if it has been frozen, and how much pectin it has. For a 9" apple pie, try 2 tablespoons of Instant ClearJel. More for juicier fruits such as berries and stone fruit.