How to export binary images

I am a neuroscientist developing a brain atlas and am using illustrator to produce the images needed.
Basically I need to open up an .ai file that contains the brain image. I need to fill that with black, remove parts of it
(haven't figured out how to do that yet) and export it at a specific location within the canvas and make the canvas a specific size.
I need to export that as a .jpeg or .gif with only 2 colors. I then need to repeat this process 700 times.
Is there a way to remove a part of an image quickly?
Is there any way to export with only 2 colors? (binary image)
Any ideas would be greatly appriciated.

1- The images are in vector format
2- I am using version 14 but will be using version 15 when my lab gets it.
3- I don't have photoshop, though I have used it and fireworks a long time ago
4-
http://books.google.ca/books?id=0prYfdDbh58C&printsec=frontcover&dq=paxinos+watson&source= bl&ots=-5jsGV_LAk&sig=fV18n7RLuPTgv9Y7rpHJ93cyi2I&hl=en&ei=ttcGTIrvCoW0lQeh0Yi-Cg&sa=X&oi= book_result&ct=result&resnum=4&ved=0CCkQ6AEwAw#v=onepage&q&f=false
or try brainmaps.org
A brain atlas is an atlas of the brain. In my case a rat brain. Not much different than an atlas you would be familiar with. It contains images and coordinates showing where areas and structures are. Since the brain is 3D a brain atlas is also in 3D. It is usually organized by having slices (think loaf of bread) placed one after another on separate pages of a book. We get the pictures in the atlas by staining the brain with chemicals that make it change colors. Then we cut it into sections on a braincutting machine and put it on a microscope slide to take a picture.
In our lab we use electrodes to listen in on what brain cells are doing. This brain atlas will allow us to show where our electrode tips were in the brain and what areas we were targeting. It is mainly for presentations and teaching.
I will be using illustrator to produce binary images of the essential stuff in exactly the right places. Once I have those I have some computer code that will stack those images together to make a 3D brain.
My biggest problem is exporting with only 2 colors in the entire image. I should be able to use my programming knowledge to take care of everything else.
I have never used any graphic vector software before so any help I can get is greatly appreciated.

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Message was edited by:
user570542

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