Help with transparency in logo

Hi all,
My company logo is an ai file (I'm using Illustrator CS4). The original logo is made up of shapes that form block letters, with white paths on top of these shapes blocking out the excess color in order to form the letters. I need to make these white paths transparent so I don't have to put a white box around the whole logo in the ai or eps version (I know when exporting to PS I can make those white paths transparent and save as a gif or tif, but I'm trying to figure out how to do this in vector). When I group all the white areas and set to no color it removes the white background, but then the red shapes that it's covering up below come through. What am I missing? Thanks so much

Without actually seeing the artwork construction, best guess is all I've got....
Select everything, Object > Expand (Or Expand Appearance, then Expand)
Pathfinder Panel > Merge
Select the white objects, delete.

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