When I submitted my application, the VFS attendant/employee took the documents out of the clearbook, both the originals and the copies. I availed the VIP service and it was no problem for her to remove it one by one and even commended that it was arranged very neatly. It took her just a couple of minutes to do that and she was really pleased she didn't have to do much other than removing them from the clearbook. If you think it would help you organized and check the documents better by separating them in the clearbook then it's up to you.
