Depending on your application you could perfuse the animal, or flash freeze the brain following rapid decapitation, and then use either a cryostat or a vibratome to slice the brain into sections and punch out the nuclei of interest.  

It depends on what method you are going to use to analyze the area.  If you are doing immuno, the perfusion would be sufficient, and provide you the best method to localize the area.  If you are doing something like western where you will be homogenizing the tissue, you'll want to decap, and punch the tissue directly.  To do this you will need to use steel matrices like the one linked.  Then you make precise cuts, identifying major structures within your R.O.I. I would also suggest flash freezing the remainder of the tissue as well just in case your cut turns out to not be as accurate as you wanted. 

http://www.stoeltingco.com/steel-brain-1-0mm.html