How to make sure a stem cell culture is cancer free?
It would not be possible to differentiate CSC from normal population non-invasively and select them out. You may do a single cell expression analysis to say if a CSC is present in a population or not but there is no magic bullet method for eliminating them. Also there are several oncogenes and some of them are also required for usual stem cell function. HAT kind of methods will not be able to eliminate potential cancer cells. Also, usual cancer chemotherapeutic drugs also affect other actively growing cell. 

Bottomline: Not possible with the current level of knowledge and technology.