Illustrator :: Merge Complex Shapes From Transparency?

Sep 3, 2012

I am using Illustrator 16.0.1.
 
I have extracted a svg model from a PDF map, which leaves me with a lot of complex shapes that are not optimised.

For example, these shapes are all composed of a lot of unneeded sub shapes. When trying to merge them together via Pathfinder > Merge, I get :

Is there a way to clean up those shapes from transparency, to get the smallest possible amount of points?

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The explanation of the reference book:
 
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<a href=[URL].....><img src=[URL]....></a>

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