Your question is incomplete . what type of cut out u want ? where u want ?
> You can create NPTH slots , holes ...of required dimension in padstack & create footprint for the same , then you can manually place that part in board where u want the cut out, it will reflect in your .drl or .rou file during drill file generation.
> If it is a irregular shape cut out manually draw it using suitable class & provide the information about this cut out in drill drawing artwork.Put all type keepout in the cut out region to avoid copper falling in this region [rout keepout /all. package keepout/all, viakeepout/all]
>If the cut outs are at the board edge controll it by board outline .
Not sure whether above line may help you requirement