I've been using BodyShop a lot recently to create clothes, however I have no use for the files that are cluttering up my Projects folder so I was wondering if it was safe to manually delete them through the windows screen? I do not want to delete the clothes i've made though, I just don't need the templates that i'm never going to use again.

No it's better to delete through Bodyshop - there are several files to get rid of, not just the folders. Go to the projects screen, load up the project and delete from there.

Or use Bodyshop Mechanic to clean up old projects. Bodyshop takes for-freaking-ever to load on my computer, so I find it much faster to delete using that. Plus if finds old projects that don't show up in Bodyshop for some reason.