1997 Honda Civic Replacing the CV Joint Boot

I am trying to replace my CV joint boots. I already removed the clamp on the boots and was able to slide them away from the cv joint. My problem is that I do not know how to seperate the cv joint from the axle. How do I get this off? Do I just need to put it in a vice and hammer at it?
Also. Since Im messing with all this will it throw off my alignment at all?. I removed them from the transmission because I was putting in a new clutch kit (bad clutch release bearing).