Blend the Nilla Wafers in a food processor until finely ground; add in the melted butter and blend until well combined. Press the mixture evenly into the bottom of the prepared pan.
In a large bowl with an electric mixer, beat the cream cheese and sugar until combined and fluffy; add in the Cool Whip and flaked coconut and continue to mix until combined. Spread evenly over the Nilla wafer layer.
Wipe out the bowl and pour in the Jell-o pudding powder and milk. Whisk vigorously for 2 minutes until thickened and set. Pour mixture over cream cheese layer. Sprinkle toasted coconut flakes over the top.
Refrigerate until completely chilled and set, about 4 hours.