If you've baked your pecan pie and the center is still runny, the best thing you can do is bake the pie for longer. This can be tricky, especially if you've already cut into the pie. If this does not help, you can turn your pie into something else, like a deconstructed dessert, or use the filling as a topping for ice cream. If you want to thicken the filling before you bake, you can add a tablespoon or two of all-purpose flour or cornstarch. This will also help the filling to set during baking.