Yes, save the file as psd so that you can have layers.
The magic wand tool will select and area in a similar fashion as the paint bucket tool fills it.
You will want to create a new layer for each country in order to animate them separately in AE. Once you’ve selected a country with the magic wand tool, select Layer>new layer via cut, and your selected piece will be cut out of the current layer and be placed onto a new layer by itself. Then you will have to select the original layer from the Layers palette and repeat for every country.