Circulating tumor cells (CTCs) have received a great amount of attention, as they are known to promote metastatic spread of cancer. Despite a wide variety of techniques developed to utilize CTCs as a diagnostic and prognostic tumor biomarker, clinical trials based on CTC analysis have shown inconsistent benefits due to difficulties in isolating these heterogeneous rare cells with high sensitivity, as well as maintaining their viability. Here, we developed a tapered slit filter (TSF) for high throughput isolation of viable heterogeneous CTCs. TSF prototypes were fabricated using a single-mask photolithography of SU-8 dry films, which were achieved by precisely adjusting UV exposure condition. The numerical analysis and in vitro cell capture assay revealed that the optimal TSF prototype was capable to reduce the stress applied on cells by 10 % compared to straight-walled slit filters (SSFs), which in turns enabled high throughput (25 mL/h), viable (87-94 %), and highly sensitive (83-100 %) capture of cancer cells, regardless of their epithelial/mesenchymal features. As a result, TSF outperformed conventional CTC isolation devices (or methods), as an EpCAM-targeting approach demonstrated low capture efficiency for mesenchymal-like SW620 cells (similar to 10 %), while sharp edges of the SSFs significantly reduced the cell viability (similar to 70 %). The clinical study using blood samples obtained from colorectal cancer patients further demonstrated that TSF was capable to isolate heterogeneous CTC subtypes, which expressed epithelial, mesenchymal, or hybrid of epithelial/mesenchymal markers. The results presented in this study support that the new device has potential to provide in-depth information on pathological status of the patients.