Install a clean Mavericks and then use TimeMachine makes it unclean again? I am about to install OSX Mavericks in an iMac I have.
I would love to make a clean install (creating the bootable USB with that complex procedure).

I was thinking about copying folder by folder but thinking about iTunes, iMovie and iPhoto makes things more complicate as they are stored in the library folder and it can carry more than one problem I guess.

I was wondering if that "clean" install will again become "dirty" if I restore everything with the copy I have in TimeMachine. 

Would that also transfer preferences and things which could interfere with the new installation?
It depends on your definition of 'dirty' — indeed, restoring from Time Machine will restore many preferences, but won't restore any system files, as they will come from your fresh OS X install.



If you want the cleanest possible OS, manually copying the files you need will be the best option — even though it's time consuming, you'll only get what you need.

The OS itself will remain 'clean' if you restore from Time Machine since the files will be kept from the OS X install and won't be restored from Time Machine.