Depending on the length, this might really be easier to do with a file. But to answer your question, yes, you can work aluminum with a router. For what you are trying to do, I would start by cutting a dado in a piece of hardwood exactly the size of your aluminum stock.

For the absolute cleanest cut use a down cut spiral bit. Even an upcut spiral bit will generally give better edge quality than a standard straight bit. A less expensive alternative to spiral cutter is to use a downshear straight bit. You can mount bearings on these if that is how your dado jig works.