You could separate the core elements of your environment and position them as camera facing planes in your scene (buildings, etc.) with another plane facing up, your ground plane. Then you'll approximately know where to place your 3d collisions and have playable characters related correctly to their environment. This is the way they probably used in old final fantasy games for example.
EDIT : this is a design trick. Basically you need to establish where the camera is and how it is looking at the ground (simply create a plane that roughly fits the proportions of a planar surface from your image and rotate and move your camera from the camera view until your 3d mesh appears to fit the corresponding 2d element).
Then you only have to place collision volumes from the camera view.
See an example below, based on a map background from final fantasy 7.
![alt text][1]
[1]: /storage/temp/6215-collisions.jpg
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