Yes, i would definetly remove them. if you have other fish, when the eggs hatch they will become food for everyone. Also, trying to raise fry in a DT is not too practical. You have to feed the fry quite a bit and that will mess up your water parameters.
I would keep the eggs in the main display until they start turning silverish, the 11th day i think it is, and then put them into a smaller tank, like an established 10gallon. use an air pump under the eggs to keep them clean. then start from there. the book "Clownfishes"
by Joyce Wilkerson is a really good read on how to raise these little guys