I also want to have PCBs made with rectangular cut-outs. Round also (ie, circular holes larger than those that can be drilled). In both cases, it is for connectors to protrude through the PCB.
With the other manufacturer I use, I send them a separate Gerber layer showing board outlines as well as internal cut-outs to be routed. Not sure how to do it here, perhaps I would need to put a diagonal cross to indicate each cut-out, which is the traditional drafting method.
Can it be done? If so, how do I indicate where cut-outs are to be made? Is there an extra cost?