Enumeration and morphological characterization of circulating tumor cells (CTCs) can be useful in diagnosis and prognosis of metastatic cancer patients. The bio-ferrograph (BF) with its five flow channels, which was developed in the late 1990s for magnetic isolation of biological cells and tissue fragments from fluids, is a modification of the analytical ferrograph. Its use for isolation of rare CTCs from human whole blood (HWB) is a novel approach for the detection of cancer at a cellular level. The isolation process is facilitated by the interaction of specifically magnetized cells with a strong external magnetic field, yielding high recovery rates with no morphological alternation of cells that are isolated on a coverslip glass slide, thus allowing complementary microscopic, chemical, biological, and mechanical analyses. Here, a full mechanical and magnetostatic design of a novel high-throughput BF is presented. The system design is based on an optimized procedure for bio-ferrographic isolation of CTCs from HWB. It incorporates a semi-automated CTC separation system consisting of sample preparation, labeling, and staining; magnetic isolation; and system recovery. The design process was optimized based on experimental feasibility tests and finite element analyses. The novel bench-top system consists of 100 flow channels, allowing simultaneous analysis of multiple samples from 20 patients in each run, with the potential to become a decision-making tool for medical doctors when monitoring patients in a hospital setting. It opens a new route for early diagnosis, prognosis, and treatment of cancers, as well as other diseases, such as osteoarthritis.