Making Instatiated GameObjects Permanent

Is there a way to "grab" gameObjects that are instantiated during the game play, and make them "permanent" in the scene (i.e. put them in the hierarchy "for real" so they show up next time you run the game)?

The goal: I'm trying to place trails of animal tracks around on my Terrain. I have the tracks set up as prefabs, basically projectors with 2 paw prints per projector. This means making large looping trails takes a long, long time. I'm pretty sure I can set up my character-controller to leave tracks (place them above the terrain with the characters position/rotation at a given interval) which would make it easy to run around and place the tracks. So, how can I "save" these sets of tracks and place them into my actual game world?

If I can't just save the gameObjects, I suppose I could just write out their positions/rotations to a text file, and instantiate them when the engine starts up. This seems like it might take awhile to load, and would be a pain to adjust if there were a few tracks that didn't look right. Being able to "grab" the objects from the game mode would be easier.

A simple solution is to have the game place the animals under one gameobject (say animals, when ready, pause the game, copy the gameobject animals (Cmd- or Ctrl-C), stop the game and paste the (now disappeared) gameobject back.