Route problem with Sub domain implementation

I have used this Web API 2 service and having a problem with its routing together with sub domains.

I'm planning to put a different copies of my Web API compiled codes in each directory, in preparation of the sub domain implementation.

For example, my working API calls looks like this

api/project/animal
api/project/animal/{animalId}
api/project/animal/count

However when putting a each copy of my entire solution inside of each different directories,
it will result a 404 (Not found error) even accessing one of them.

How can make it work to have a dynamic prefix route such as

newDirectory/api/project/animal
newDirectory/api/project/animal/{animalId}
newDirectory/api/project/animal/count

anotherDirectory/api/project/animal
anotherDirectory/api/project/animal/{animalId}
anotherDirectory/api/project/animal/count

Information about the implementation: I'm using attribute routes [Route("")] for route specifications.