1) add an inductor between Vcc and Avcc -> see Atmel Documentation
2) As Aref pin from the board output connector can't be move because existing shields, Aref link have to be improve.
A) add a 100nF capacitor as close as possible from the microcontroller
B) insert an inductor in the link between the microcontroller pin and the Aref output board connector. This will make a filter with the existing capacitor.