Atom chips are micro-fabricated devices which create versatile magnetic potentials for trapping, cooling and controlling ensembles of ultra-cold atoms. Advancing from the typical atom chips, currents from superconducting vortices are used to trap and manipulate the ultra-cold atoms in our experiments. The superconducting vortex traps can be configured by controlling strength and pulse time of external magnetic fields together with bias fields. In order to fully utilize reconfigurability, superconducting vortices are optically manipulated with laser light to generate desired vortex patterns with this tailored trapping potentials for ultra-cold atoms are created. We have carried out heat diffusion simulations of laser patterns and characterized laser power and pulse time to effectively configure the desired vortex potentials. We have also successfully manipulated vortex matter optically to create arbitrary vortex patterns and ring potentials for cold atoms to utilize in quantum simulations and on-chip matter wave interferometry applications. Moreover, cold atoms could be used as a sensitive probe to examine magnetic field distribution of the superconducting vortices and we have used this technique to experimentally verify the resulting magnetic potentials of superconducting vortices after optical manipulation. v First of all, I would like to express my heartfelt gratitude and appreciation to my teacher and mentor, Prof.