Graynomad pinout diagram plus Sam3x datasheet are a good starting point to learn how to access timers, interrupts,etc...Search in the DUE sub forum for example sketches and/or relevent libraries, e.g.:https://forum.arduino.cc/index.php?topic=537586.0
For example, the register TC_CMR0 for the timer/counter2 can be accessed in the IDE by the name REG_TC2_CMR0.
Hi there @alirazaviarduino,If what you want is just to generate a PWM signal with the DUE, you have library pwm_lib (https://github.com/antodom/pwm_lib), 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 (https://github.com/antodom/tc_lib), available for the DUE. Here the same, have a look to the library's documentation and examples.I hope it helps.