Click on the object you want, then hit the clipping tool (The square cut into a slope) and draw a line on the maximum height you want the rectangle to be. Keep clicking it until both sides of the line are white, then hit enter. Now, click the selector tool, and clipping tool again. This time, make the line on one side of your rectangle, and again, you want all white on both sides. Finally, repeat step 2, but for the other side, click the selector tool (and make sure you're selecting solids instead of groups), and click the rectangle you made. From there, hit delete, and you have a rectangular hole