How can I change the amplitude of a pwm signal ?

CrossRoads:
You get 0V, you get 3.3V. That's it. You want a level in between you need external hardware. 2 resistors as a voltage divider as minimum.

I believe the Due actually has two digital to analog converters (as opposed to just PWM), which can be used to provide a changing voltage at the output pin. With these there really isn't a need for PWM, and no external hardware is needed, PB15 & PB16