Combine the flour, brown sugar, and salt in a medium bowl. Add the butter and mix with a pastry blender or your fingers until the mixture forms crumbs that hold together when pinched. Mix in the pecans.
Set aside about 3/4 cup of the crust mixture to use for the topping.
Press the remaining crust mixture into the bottom of an 8-inch square baking pan. Bake 12 to 15 minutes, or until lightly browned.
To make the filling:
Using an electric mixer on medium speed, beat the cream cheese, sugar, milk, and vanilla until thoroughly combined and smooth.
Spread the filling mixture evenly over the partially baked crust.
Sprinkle the top of the filling with the reserved crust/topping mixture. Lightly press the topping into the filling.
Bake 30 to 40 minutes, or until the filling is set.
Cool completely. Cover and chill for at least an hour before cutting into bars.
Notes
Store the bars in an airtight container or wrapped well in plastic wrap up to 5 days in the refrigerator. Wrap the bars well in plastic wrap and place in a freezer-safe container for up to 3 months in the freezer.