Ok, here's a detailed blueprint of what I meant.
Backdrop Tiles
These tiles are just for decoration. Link cannot interact with them.
>Outdoors
-Folders based on location (Mountain, Water, Field, Village, Desert)
>Indoors
-Folders based on type of building (House, castle, jail, dungeon, etc)
Active Tiles
These are the tiles Link can interact with. Anything ranging from collisions to using items to lifting, to cutting with a sword, etc. Most of the tiles will probably be active tiles.
>Outdoors
-Folders based on location (Mountain, Water, Field, Village, Desert)
>Indoors
-Folders based on type of building (House, castle, jail, dungeon, etc)
The tiles would be named with appropriate names and all in .png format unless animated.
(Bush tile would be named "Bush", etc), (Animated tiles would be named as such: greenrupee1, greenrupee2, greenrupee3, etc. One file for each animation frame)
*I realize that in some cases custom tiles will need to be made. In the event of this I will create in image of the map I'm tryng to replicate and post it here.