I have removed glued down carpet from cement, can I install the thin set over the mastic?

No, you must scrap it off first. Mastic never hardens fully but thinset does and needs a sound base. I used a specail tool, Spider Scraper, that attaches to my reciprocating saw to speed it up. Spyder Products | Tools You'll Love For The Jobs You Don't (http://www.spyderproducts.com/)