We demonstrate an attractive nanomachine 'capture and transport' target isolation strategy based on molecularly imprinted polymers (MIPs). MIP-based catalytic microtubular engines have been prepared by electropolymerization of the outer polymeric layer in the presence of the target analyte (template). Tailor-made selective artificial recognition sites have thus been introduced into tubular microtransporters through complementary nanocavities in the outer polymeric layer. The new microtransporter concept is illustrated using bilayer poly(3,4-ethylenedioxythiophene)(PEDOT)/Pt-Ni microengines and an avidin-FITC (Av-FITC) labeled protein as the template. The avidin-imprinted polymeric layer selectively concentrates the fluorescent-tagged protein target onto the moving microengine, without the need for additional external functionalization, to allow 'on-the-fly' extraction and isolation of Av-FITC from raw serum and saliva samples along with real-time visualization of the protein loading and transport. The new micromachine-MIP based target isolation strategy could be extended to the capture and transport of other important target molecules towards diverse biomedical and environmental applications.