We show optical tweezers manipulation of individual micron-sized samples investigating at the same time their inner nanostructure by synchrotron diffraction experiments. The validity of this technique is demonstrated for clusters of multilamellar liposomes trapped in single and multiple positions in the optical path of a microfocused x-ray beam and analyzed in a microscanning mode. The signal to background ratio of the first order peak shows that single liposome measurements are feasible. Multiple trapping by means of diffractive optical elements is demonstrated as an effective manipulation tool for future x-ray diffraction studies of the interaction between different sample entities.