Prepare muffin pan by generously greasing (with softened butter or shortening) and flouring each muffin cup (or coat with a flour-based baking spray, such as Baker's Joy).
In a medium bowl, beat together cream cheese and butter. Mix in flour until smooth and well combined. Scrape dough onto a sheet of plastic wrap, wrap and form into a disk, and refrigerate for 30 minutes to an hour.
In another medium bowl, beat butter into brown sugar. Blend in eggs, vanilla, and salt, and mix until thoroughly incorporated. Gently stir in pecans.
Place oven rack in center position of oven and preheat to 350°F. Once dough is chilled, divide it into 12 equal pieces (I do so by forming a circle with the dough, cutting it into quarters, and then dividing each quarter into three pieces...if you have a small kitchen scale, it can help you achieve equal pieces, but eyeballing it works, too!). Roll each piece of dough into a ball and use your fingers to gently press it into a thin, flat circle. Lay the circle of dough in one of the greased and floured muffin cups and gently press it into the bottom and up the sides, spreading the dough a bit more if necessary to cover the entire cup. (You want the crust to lightly adhere to the muffin cup, but don't press it too hard or it may get stuck!)
Give the filling another stir to redistribute the pecans and evenly divide it between the 12 mini pie crusts (use a cookie scoop to make this easier).
Bake for 20 to 25 minutes or until filling is puffy and set. Remove pan to a rack and allow to cool for 2 minutes. Run a thin knife around the edges of each muffin cup to make sure that there is no sticking. Allow to rest for 5 more minutes. Run knife around each pie one more time. Place a cooling rack on top of muffin pan and carefully invert so that pan is resting upside-down on rack. Carefully lift pan and turn the pies over to finish cooling on the rack.
Dough may be made up to 3 days in advance, but you will need to let it soften at room temperature enough to form it into individual pie crusts (but make sure it is still somewhat chilled or it will be too soft and sticky!).
The trickiest part of this recipe is removing the pies from the muffin pan, but it definitely can be done! The keys to success are making sure that the muffin cups are thoroughly greased/floured, initially loosening the pies with a knife, allowing them to set long enough that they don't fall apart, once more making sure that they're loosened, and then putting the cooling rack on top of the pan before carefully overturning.