The postman brought me a second-hand 20" remchoked cantilever barrel today.  I was psyched until I slide the thing on and it doesn't go down all the way.

It appears that the end of the extension is tweaked up at the end ever so slightly which is causing the cut-out to be pinched a little bit at the opening.

Is this barrel toast or can I file off a little material so there is enough clearance?

Thanks in advance to any of the resident shotgun sages out there who can help me out with this!

Since it's a used barrel, and I'm assuming you can't return it for a exchange or refund, you have two options.
One it to send it to Remington for a repair.  I'd bet that they'll fix it for no charge.

Second is to go ahead and do some filing.  I'd look things over REAL well to be sure I was filing in the right area.
Comparing it to a good barrel will help.

Thanks DF!

Compared to my other barrel, it seems just a tiny bit off and I bet I could even things out pretty easily.

Assuming I don't remove to much material and that's all it takes to get the fit right, should everything be reasonably OK from that point on or do I risk seriously comprimising saftey or alignment by modifying the notch in this way?

If you're referring to the notch that fits over the ejector assembly, and the barrel is deformed enough that it won't slip over, I don't see any problem with filing it just enough to clear properly.

This is based on my NOT seeing the damage, so you're on your own.