CAN Communication

I am designing a User interface that controls the input parameters and displays them on an LCD.

There will be 2 microcontrollers and one FPGA connected via CAN communication. Is it advisable to use Arduino Due for this? If so, then which transceiver should i get and will it available in element14 or mouser?

If not, then what microcontroller should i choose?

That is a pretty open ended question. Is it advisable to use a Due? Well, sure, as long as you're comfortable with that board. You should use what works for you. It pays to stick with what you know as the learning curve is easier. If you're freshly starting out then your options are more open. The Due is very capable but at one point it was discontinued. It seems to be available once again. Personally, I really like it. I'm sure a Due would work fine for what you say you want to do with it.

As for transceiver, get something in the SN65HVD230 family. There are multiple chips that differ only in the last number (230, 231, 233, 234, etc). Pick the one that makes the most sense for you. They have different options. They should all be available wherever you want to buy parts from.

But, first and foremost, use a processor you are familiar with if at all possible.