iCloud Removal of Downloads not showing for local files

I am having an issue where some of my files are downloaded with the majority of them sitting in the cloud and I want all my files to go into the cloud only and not stored on my Mac. I am a web developer and I have loads of files and I am finding it very time consuming having to go into each and every directory to remove the downloads of certain files. I have included a screenshot and as you can see for an example in the right most column I have 4 files that have been stored locally, however if you look at the the icons it tells me the files are in the cloud, but some of them are not, they are stored locally (you can right click on these and select Remove Download). Anyone know how to easily remove these downloads without having to go into each and every directory (there could be 100s of folders and 1000s of files). Remove Downloads from the context menu is not available from the root folder so it can't be done that way either. Re-downloading and resetting all of them again is not an option as I have over 90GB and 100000s of files and it literally takes 3 days to do that. Any ideas?