It looks like you've got something like that indicated, but not highlighted. Open up the "Regions" tab, select the rectangle, and make sure it appears in the box before closing it.
For the circular pocket, you can use the edge of your cylindrical hole as a Region - try the "Dupedge" command in Rhino if you don't have a circle there to highlight.
If you don't want to cut your part free, try making some tabs (with Rhino's Box command) that connect the part you're cutting out to the stock surrounding it. They can be lower than the part itself, to make removing them easier. Make your Region a rectangle that is far enough from the edge to give you room for the tool, but that doesn't include the whole length of your tabs, so it won't cut them off.
Andrew Werby
www.computersculpture.com