Abstract: The present invention relates to improved techniques for separating cells, particles and molecules important to medical science and biotechnology because separation is frequently the limiting factor for many biological processes. The apparatus and method of use provides an innovative method for quantitatively separating cells, proteins, or other particles, using multistage, magnetically, electromagnetically assisted separation technology, (“MAGSEP”). The MAGSEP technology provides a separation technology applicable to medical, chemical, cell biology, and biotechnology processes. Moreover, the instant invention relates to a method for separating and isolating mixtures of combinatorial synthesized molecules such that a variety of products are prepared, in groups, possessing diversity in size, length, (molecular weight), and structural elements. These are then analyzed for the ability to bind specifically to an antibody, receptor, or other ligate.