A thermal annealing technique for Nb/Al-AlOx/ Nb Josephson Junction based on selective laser heating is presented. This technique allows locally modifying the Josephson critical current density profile in a junction. The localized heating inside a single circuit element with a good spatial resolution (less than 1micron) is made possible by depositing a carbon film on the desired region exploiting the larger absorbance coefficient of Carbon (close to 1) respect to Niobium (about 0.2). The selected junction is then uniformly exposed to an Ar laser beam aligned by an optical system. The different power absorbed by the different surfaces under irradiation allows to reach higher temperatures under the carbon film than in the surrounding areas, leading to a selective annealing. Critical current measurements on high quality Josephson junctions have shown a reduction of the total critical current. Magnetic pattern measurements evidenced that the critical current density was changed only in the absorber covered region, leaving unchanged the critical current density outside that region ensuring the capability to locally modify the Josephson critical current density. This technique paves the route to the control of critical current density profile and/or to the production of controlled “defect” inside the junction area.