Cancer cell presents a dynamic nature that evolves over time in its microenvironment through a complicating molecular and cellular interaction network. Despite the progress already achieved in the imaging technologies and the molecular tools used for tumor cell diagnosis and treatment approaches, metastasis still remains a major hindering factor that limits the clinical outcomes. Circulating tumor cells (CTCs) present the potential in providing critical information to understand the metastasis process, the tumor cell and genome heterogeneity, in a way to overcome cancer therapy bottlenecks and improve the efficacy and safety therapeutic profiles. The experience already gained shows that CTCs as tools possess a predictive biomarker capacity by aiming the understanding of most of the known cancer cell hallmarks at the molecular level, as well as the translation of the extracted relevant knowledge in clinical practice. The efficient isolation and characterization of CTCs might reveal the intratumoral heterogeneity present in tumors while providing critical insights into cancer metastasis. Moreover, by combining the emerging single cell omics technologies, CTCs can be valuable biological source material to unveil the existed intratumoral cellular and genomic heterogeneity, as well as to pharmacologically exploit critical knowledge for the validation of prognostic and diagnostic biomarkers within the concept of precision and personalized cancer therapy. In this article, a novel combined methodology for the isolation and detection of CTCs based on flow cytometry and cellular filtration technologies is presented.