You can use FACS to isolate CSCs if the machine has the sorting system. Labs that do not have it use magnetic cell separation method to isolate cancer stem cells. It is much cheaper and also very efficient technique. 

You can find the link to the system I use here,

http://www.miltenyibiotec.com/en/products-and-services/macs-cell-separation.aspx

There are few ways in which you can do

Anchorage independent assays, flow cytometry, sphere formation assays, animal transplantation assays

antibody mediated cell sorting using FACS is d best way to get csc. You can go for pure line after cell culture if possible.

You can use CD44+/ESA+/CD24- as a biomarker for isolation of cancer stem cell from breast tissue by FACS sorting.

I believe you have two sequential method together to make sure about the quality of your purification. For example anchorage independent and then FACS together. Then you will have a pure fraction of stem cells.