The conventional techniques to detect circulating tumour cells (CTCs) are lengthy and the use of centrifugal forces in this technique may cause cell mortality. As the number of CTCs in patients is quite low, the present study aims towards a gentler diagnostic procedure so as not to lose too many CTCs during the sample preparation process. Hence, a Three-Dimensional Microwell dialysis (3D-μDialysis) chip was designed in this study to perform gentle fluorescence-removal process by using dialysis-type flow processes without centrifuging. This leads to a minimum manual handling of CTCs obtained in our study without any contamination. In addition, a rapid staining process which necessitates only about half the time of conventional techniques (35 minutes instead of 90 minutes) is being illustrated by the employment of dialysis process (by dynamically removing water and waste at once) instead of only static diffusion (by statically removing only waste by diffusion). Staining efficiency of our technique is improved over conventional staining because of the flow rate in 3D-μDialysis staining. Moreover, the staining process has been validated with clinical whole blood samples from three TNM stage IV colon cancer patients. The current technique may be termed as "miniature rapid staining and dialysing system".