antodom:
Hi there @alirazaviarduino,If what you want is just to generate a PWM signal with the DUE, you have library pwm_lib (GitHub - antodom/pwm_lib: This is a C++ library to abstract the use of the eight hardware PWM channels available on Arduino DUE's Atmel ATSAM3X8E microcontroller.), a library that was designed and developed specifically for that using the DUE. Have a look to the examples coming with the library and its document to start with.
As to timers you have another library, tc_lib (GitHub - antodom/tc_lib: This is a library to take advantage of different functionalities available on Timer Counter (TC) modules in Arduino Due's Atmel ATSAM3X8E microcontrollers), available for the DUE. Here the same, have a look to the library's documentation and examples.
I hope it helps.
Thanks antodom.