Here is an example of a header tube being modified.

Clearancing headers is standard procedure on combination where a production headers don't fit exactly how you might want.

This example is on a '69 small-block Chevelle with a kickout Moroso pan. The header tube was just barely rubbing the paint off of the header, and probably heating the oil inside the pan. My friend asked if there was a way to fix this without pressing the tube flat in that area. I told him, let's find out!

I started by marking on a piece of paper the original path of the tube so we know how much we've changed it without needing to re-install the headers. 

It needed to go in about 1/4 an inch at the point where it touched the pan, which we marked with a sharpee.

To make a tube go in, you need to take material out of the inside half of the tube to create a relief area. The other cut is where some material will be removed all the way around the tube's circumference but more on the outside to allow it to bend inwards.

When it's all done, it was an easy weld and grind job to make it smooth and look as if nothing had ever happened. You'll need to coat or paint the tube after this minor surgery to make sure it doesn't rust.