The current study presents an innovative magnetic bead-based 3-dimensional (3D) micro-incubator for rapid purification of tumor cells (TCs) by using micro-electro-mechanical-systems (MEMS) technologies. With the incorporation of magnetic beads, specific antibodies conjugated onto the surface of the magnetic beads can be used to specifically recognize the TCs in the clinical body fluids, followed by collecting and purifying them with the incorporation of a magnet and built-in microfluidic control module. The novel 3D micro-incubator was developed for incubation and mixing process in the purification process when a relatively large amount of bio-sample was required. The vortex effect can be generated within the incubation chamber such that large amount of clinical bio-samples (∼ 1000 μl) can be mixed efficiently within a short period of time (less than 10 minutes). In addition, successful demonstration for detection of ovarian and lung cancer cells has been achieved by performing an on-chip genetic identification. As a result, magnetic bead-based 3D micro-incubator integrated with microfluidic modules may provide an automatic platform for rapid purification and fast detection of cancer cells.