An apparatus and method for performing a magnetic cell separation process using paramagnetic beads, and having multiple steps or activitites which are required to complete the process successfully includes using a programmable machine (10) to either perform selected ones of the multiple steps itself; or to prompt a human attendant to perform others of said steps in sequence and to thereafter provide to the machine a verification input that the step to be performed by the human attendant is completed. The repeatability and reliability of the process when performed by the programmable machine (10) is vastly improved in comparison to conventional laboratory practice. Additionally, the programming of the machine (10) may be altered by super visory personnel to improve the efficacy of the process, or to customize the process for the separation of a particular type of cell.