Circulating tumor cells (CTCs) are important biomarkers which can be used for early-stage cancer detection and treatment. Developing an efficient approach to detect CTCs from peripheral blood is a challenging problem due to their extreme rarity. The CTC microfiltration provides a good solution as a critical method based on the physical property of CTCs. In this study, we employed a compound droplet model to investigate the transport behavior of a CTC squeezing through a conical-shaped microfilter. The compound droplet model of CTC is composed of a cortical membrane, cytoplasm and the nucleus. Numerically, we used the octree-based Adaptive-Mesh-Refinement (AMR) to analyze the deformable CTC flowing through a microfilter with non-uniform cross-sections. We investigated the pressure-deformability behavior of the cell with different nuclear to cytoplasmic ratio (N/C ratio). Our study revealed that the nucleus smaller than the filter pore did not affect the pressure behaviors significantly. However, when the nucleus is larger than the filter pore size, the pressure behaviors are greatly affected. We also studied the effects of the flow rate on the cell squeezing process. We found that the critical pressure increases significantly with the flow rate. Our study can provide valuable information about cell transport behavior in conical-shaped microfilters.