Metalworking is a hobby of mine, so I'd probably just use a milling machine
Not having that (or if it's inconvenient, etc) the next choice would be to drill or punch a couple of small holes in a straight line and then file the edges flat so you have the correctly shaped opening. Time consuming, but without the right tools, it's not trivial.
Since it's generally easier to drill or punch a round hole, I tend to prefer round connectors. You can find micro usb connectors that are designed for round openings. Search "micro usb round panel mount." Of course, they will cost more.
What you can also do if you're using a clamshell case and you can align the connector with the area where the two halves come together, is to use a file or a nibbler to make an opening on one or both edges. Sometimes this is easier.