The Active Rectangle can easily be seen in Full View as a dotted rectangle. In magnified view it is all of what is visible. You can set it in Normal or Full Views by dragging a box around an area.
In addition to this, pressing A shows Full View, saves the old Active Rectangle, and makes the whole picture Active. Notice the odd looking borders around pictures in CombineZ5. If you press A again, the Selected Rectangle jumps inwards to remove part or all of this border. The Active Rectangle now represents the original pictures' size that was loaded from disk. Because of shrinkage due to resizing and displacement due to lining up the Frames, this may not be enough to completely remove the unsightly border. Press A a third time and the Rectangle jumps further in to where it considers the Dirty Border finished. Treat this as a suggestion; the program may get it wrong. One more press on A and the original saved Active Rectangle is restored and the cycle begins again.
If you use Save Frame/Picture, the item is saved in its entirety regardless of the Active Rectangle.
If you use Save Rectangle As, only the Active Rectangle is saved. This is how to save a cropped picture. This command saves whatever is on the screen, so you can save a picture of a Plane or the Depthmap. You are also given the opportunity to rotate this picture in 90 degree steps as it is saved.