Chosen Solution

Is it possible to remove the cd drive out of my MacBook Pro late 2009 and add a 2th harddrive.

yes, take a look at this article - There are a couple companies (like this one and this one) now making brackets to install in the optical drive slot, you can put a 2nd hard drive or SSD there

so the optical drive is the same size in the 2006 model as mine late 2009