Preheat the Oven: Preheat the oven to 350°F.
Prepare the Pumpkin Filling: In a medium bowl, whisk together the pumpkin puree, brown sugar, salt, and 3/4 teaspoon of the pumpkin pie spice until well combined. Set the mixture aside. Make the Spice Sugar: In a small bowl, stir together the remaining 1/4 teaspoon pumpkin pie spice and the granulated sugar.
Arrange the Fillo Shells: Place the thawed mini fillo shells on nonstick baking sheets, arranging them so they are ready to fill.
Layer the Fillings: Sprinkle a small amount of the pumpkin pie spice-sugar mixture inside each fillo shell. Add a few pieces of chopped pecans, followed by one cube of cream cheese. Spoon a heaping teaspoon of the pumpkin mixture into each shell. Finish the Cups: Sprinkle any remaining pumpkin pie spice-sugar mixture over the filled shells.
Bake the Strudel Cups: Bake at 350°F for 15 minutes, or until the fillo shells are golden and the cream cheese has melted.
Serve Warm: Serve the pumpkin pecan strudel cups warm, adding a dollop of whipped cream if desired.