Aptamers have been regarded as promising artificial antibodies with high stability. To successfully select aptamers that were able to be directedly adopted for clinical applications, we have developed an integrated microfluidic chip to perform a tissue-based SELEX (tissue-SELEX) in which time and processes of SELEX were reduced and simplified. However, our previous design required a large number of tissue specimen and chips fabricated for individual rounds of SELEX. Moreover, many aptamers targeting cytosolic or nucleus proteins were selected through tissue sections that could not be used in membrane-specific target therapy and diagnosis. In this work, we reported the first automatic microfluidic system which was capable of performing "continuous" SELEX with clinical "tissue" samples, which only took 12 hours to complete 6 rounds of SELEX with minimum volume of tissue samples and reagents. In addition, in order to further improve the selection outcome, a single-stranded DNA (ssDNA) library specific to the cell membrane was pre-selected such that the screened aptamers could be specifically bounded on the cell surfaces for targeting and diagnostic applications.