In this study, surface acoustic wave (SAW) systems are described for the removal of molecules that are unbound to micromotors, thereby lowering the detection limit of the cancer-related biomarker miRNA-21. For this purpose, in the first step, mass production of the Au/Pt bimetallic tubular micromotor was performed with a simple membrane template electrodeposition. The motions of catalytic Au/Pt micromotors in peroxide fuel media were analyzed under the SAW field effect. The changes in the micromotor speed were investigated depending on the type and concentration of surfactants in the presence and absence of SAW streaming. Our detection strategy was based on immobilization of probe dye-labeled single-stranded probe DNA (6-carboxyfluorescein dye-labeled-single-stranded DNA) to Au/Pt micromotors that recognize target miRNA-21. Before/after hybridization of miRNA-21 (for both w/o SAW and SAW streaming conditions), the changes in the speed of micromotors and their fluorescence intensities were studied. The response of fluorescence intensities was observed to be linearly varied with the increase of the miRNA-21 concentration from 0.5 to 5 nM under both w/o SAW and with SAW. The resulting fluorescence sensor showed a limit of detection of 0.19 nM, more than 2 folds lower compared to w/o SAW conditions. Thus, the sensor and behaviors of Au/Pt tubular micromotors were improved by acoustic removal systems.