This study reports new three-dimensional (3D) micromachined magnetic tweezers consisting of micro-electromagnets and a ring-trap structure, fabricated using MEMS (micro-electro-mechanical systems) technology, for manipulating a single 2 nm diameter DNA molecule. The new apparatus uses magnetic forces to exert over 20 pN with less heating, allowing the extension of the DNA molecule over its whole contour length to investigate its entropic and elastic regions. To improve the localized DNA immobilization efficiency, a novel ring-trapper structure was used to handle the vertical movement of magnetic beads which were adhered to the DNA molecules. One extremity of the DNA molecule, which was bound to the thiol-modified magnetic bead, could be immobilized covalently on a gold surface. The other extremity, which was bound to another unmodified magnetic bead, could be manipulated under a magnetic field generated by micro-electromagnets. The important elastic modulus of DNA has been explored to be 453 pN at a low ionic strength. This result reveals that DNA becomes more susceptible to elastic elongation at a low ionic strength due to electrostatic repulsion. The force–extension curve for DNA molecules is found to be consistent with theoretical models. In addition to a single DNA stretching, this study also successfully demonstrates the stretching of two parallel DNA molecules.