Before brining in my animation to tale out the rig I exported a single frame of my animation without the rig. I then brought both my animation and picture into After Effects with the picture on top and animation below.
At the point in the animation where the rig is seen I made a mask on the picture layer around the rig. This meant that rig is covered by the section of the rig I masked off. I then needed to do this for each frame that the rig is seen.
Then when I export the animation the rig is no longer seen.
I also used After Effects to add shakes and glows to my animation. These helped to tell the story and add special effects to enhance my Stop-Motion animation.