The colours provide contrast. It makes it much easier for a doctor to find the parts they are interested in as quickly as possible. Not to mention the fact that

The colours provide contrast. It makes it much easier for a doctor to find the parts they are interested in as quickly as possible. Not to mention the fact that doctors aren't always interested in the tiniest imperfections and may be looking for large changes. When you have things segemented out and coloured, it is also much easier to view the object, be it an organ, blood vessel, etc. in 3 dimensions, which is something that is very useful. Admittedly, they can get in the way sometimes, but that's why it is an optional feature.