When working on the Flash timeline, you will need two layers for this animation (plus the background layer if you have a background graphic).
The background graphic layer is the bottom layer in the Timeline. Then you will have the ball on its own layer just above that. Then you will have the tree on a third layer above the ball layer.
Because the ball is on a layer under the tree layer, it will disappear when it passes under the tree.
If your tree is part of the background layer, you will need to make a copy of the tree to put on the tree layer. Use Photoshop or some other graphics program to select the tree and copy. Start a new image window and paste the tree on a new transparent layer. Save file. Then you can import the tree psd into Flash.
Hope this helps,