Is it possible to create a PCs with a ground plane on the bottom then three separate planes on the top layer, for say 3V, 5V and another common connection?
Yes, there are several ways of making three separate planes. i.e. Take the Copper Fill Blocker and stretch it into a lone line from top to bottom. You can extend it past the pcb if you want. Set to fill top layer, set your ground seeds to your power supplies in each section, then click Routing/Ground Fill (top).