This paper reports a systematic study of the Capillary number (Ca) effect on cell viability in Microfluidic Elasto-Filtration (MEF) devices for ex vivo circulating tumor cell (CTC) isolation. CTC viability decreases with increasing Ca because of the higher hydrodynamic shear stress. CTC viability also decreases with increasing cell diameter to filter-pore size ratio, d*, due to the larger interaction forces between cells and filter pores. The cell viability dependence on Ca can be well fitted by two distinct functions for two ranges of d*, larger and smaller than 2.5. Together with previously reported Ca effects on CTC capture efficiency and depletion of white blood cells, a complete design rule for MEF chips is proposed, yielding 92% CTC capture efficiency, 4-log WBC depletion, and 85% CTC viability at an optimized Ca*.