Its possible to safe MLVs in different Folders. Thats fine for a quick workflow on a small project.
It will be nice to have all MLV Files in an extra Folder anyway. Coping on PC is easyer. When its in an archive and there are hundreds of CR2´s in the Folder because timelaps f. e. - then is one folder with all MLV Files in there verry good too.
And it looks more professional when there is a folder named MLV_RAW_OUTPUT ;)