1) Long clean times may be caused by a low memory situation in e2studio- check available memory on your PC.
2) Soft errors and retries on the disk file system- see if a disk check shows any issues and fix them if it does.
3) It's also possible that the include paths in the project may have invalid search paths or paths pointing to other systems that may not be available or on networked drives- check your include paths to make sure they are correct.
4) After checking the above, try re-launching e2 studio and see if it speeds it cleaning. If not, delete the debug directory in the project (this is a full clean operation!).