I cut out the door openings using air nibblers after the side skins were attached. I drilled a small 1/4 inch hole in the lower from corner from the inside out so I could have a starting point in the exact location I wanted. I then proceed with the cut from the outside using the the wall as guide on the blind side. The painters tape you see in the photo was used to prevent scratches from the cutting tool.
You can also use a router, but you will need to slow the cutting speed down using a speed controller of the bit will do more melting than cutting. The second photo shows the router method being used to cut out the window openings. The router method results in a more finished flush cut, but the downside is the aluminum chips it creates. You will find these chips everywhere for weeks afterwards.
