This is how I cut and fit tubes together - called variously coping, notching, or mitering, depending on what dialect of English you grew up with.
Our demo tube today is Keith's top tube. I'm mitering the top tube where it fits against the seat tube.
Step one is to rule a line down the tube - this is used to keep the miters "in phase", so that things line up when you assemble the bike. I like to put the lines along the top of the top tube, top of the down tube, and front of the seat tube. That allows me to line up lug points nicely, and also gives me a reference line for bidon cage mounts.
Go to your CAD tool and put a dimension line along the point on your drawing where your ruled line would be. We're doing the top of the top tube, so the dimension is shown below (the 509mm one):
Your tube will generally have a little red paint on one end, and the other end plain. The paint indicates the shorter butt, so position the marks so that they're up towards that end of the tube, so that you'll be cutting most of the material from the unpainted end. Don't forget to leave some allowance for the tube to wrap around at the sides.
Next, I download a copy of tubemiter, by Giles Puckett, and type in the specs for the miter I'm doing. I print the result on sticky address label paper. I cut that out and wrap it around the tube, so that the top of the miter is accurately aligned with the cut marks. Be careful to get the phase right - it's incredibly embarrassing to miter both ends of a tube only to find that one is upside down.
Now that I know the shape to miter to, I start by making a pair of cuts in the tube with a hacksaw. I get a little closer each time I do one of these.
Flip it over and do the other side, and you end up with a nice little cutoff piece that you can show to all your friends.
Finally I take to the tube with a file. For this miter I used a 200mm long half-round 2nd cut file. One of these days I'll buy some bastard files to speed up the process, but the 2nd cut files work quite nicely. For head tube miters I use a 250mm file.
And that's it. All in less time than it would take to set up a mill to do the work.