This paper reports tapered-slit filters (TSFs) for the high-throughput and viable separation of heterogeneous circulating tumor cells (CTCs) with epithelial, mesenchymal and hybrid expressions. The tapered-slits, whose inlet widths are wider than outlet widths, not only increase the capture ratio of CTC-to-WBC, but also reduce the cell stress applied by hole-entrance; thus achieving high-throughput and high-efficiency CTC isolation remaining viability. Demonstrated is TSFs' capability to detect heterogeneous CTCs and clusters using colorectal cancer patients' blood samples with low PBS dilution without RBC lysis. TSFs' capability for the rapid and viable isolation of heterogeneous CTCs enables to diagnose patients more precisely for more appropriate treatment.