We developed a novel technique to manipulate lipid nanotubes in 3D by laser tweezers in water solutions. Laser tweezers are well known as one of the noncontact manipulation methods used in a closed space. We reported on 3D 6DOF manipulation of microbeads using 3D Synchronized Laser Micromanipulation (SLM), however, the blur is generated in the microscope image when multiple points at different height are trapped by scanning the focal point of laser. Moreover, it is difficult to manipulate a nano scaled rod-like object stably in 3D, since optical trap force is weak. To manipulate a lipid nanotube for example, firstly, we newly developed an observation system to improve blur of image by synchronization of shutter timing of CCD camera and laser scanning. As a result, we can obtain a clear image of the targets at different height while manipulating them. Secondly, we developed functional gel microtools which can adhere to the lipid nanotubes. We succeeded in controlling the position and orientation of the lipid nanotubes by using 3D SLM with shutter timing control method and novel functional gel microtools.