I'm guessing you're staining for atherosclerotic plaques in the aorta.  I've used saturated Sudan Black B in 70% EtOH to stain for plaques in rabbit aorta.  The samples are then destained with several washes of 70% EtOH.  The plaques show up as dark blueish-black through the more superficial tissues.  Works well, just keep an eye on the destaining.  I then further processed portions of this tissue for histology (paraffin embedding) with no adverse affects (that I could see).
 

Albert C. Grobe, MS
Tissue Engineering Lab
International Heart Institute
Missoula, MT