Sub uS PWM Resolution on Due/SAM3X with Interrupts

I need to drive some existing hardware with Pulse Widths that have an ideal absolute minimum width of ~40nS. If that's not possible then 400nS Pulse Width would be the fallback and for my purposes would be an amazing time saver. I alread

The hardware itself is a HV PWM Signal Generator and I need a way to automate the timing so I don't have to babysit the machine. It is driven with a 5V signal into a 50Ω load and I already have a circuit that works for that purpose. I just need to be able to reliably drive it.

I'm wondering if a library exists that is compatible with the Arduino Due that will allow me to create an ISR that will execute based on a Timer that can be configured to run at intervals faster than 1uS.

I thought I found what I needed in the DueTimer Library but evidently I need something a bit faster.

I have some experience with the ATMega2560 and had just gotten used to setting the Timer registers for fastPWM. That took me an embarrassing amount of time on its own and I'm hoping to leverage the experience of someone that has done something similar so I don't spend 2 more weeks figuring out which registers will let me create a PWM signal with pulse with and duty cycle that I can control with a button matrix and rotary encoders.

The most important specification and hurdle for me at this moment is getting to know the SAM3X Timer Registers.

Resources I've got open:
Sam3X Datasheet
Arduino Due Timer Blocks
Arduino Due Pin Mapping SAM3X

criticalpoint:
The hardware itself is a HV PWM Signal Generator and I need a way to automate the timing so I don't have to babysit the machine. It is driven with a 5V signal into a 50Ω load and I already have a circuit that works for that purpose.

Glad to hear that you could master the first step of your project. Why do you open a new thread?

Why do you think that you need an ISR for generating pulses? Repeated pulses of the same frequency don't require manual intervention.

A 16MHz controller can generate PWM pulses up from 62.5 ns width. Width and distance or frequency is adjustable independently in 62.5 ns increments.

The UNO, NANO, Leonardo, Micro, and MEGA run at 16 MHz so you can get 14 different sub-microsecond pulse widths. What input are you using to "automate the timing"?

An ISR can be delayed if another interrupt is still being processed. You would get a better signal if you let the hardware turn the pins on and off.