A method and system for removing mortar from a plurality of joints between a plurality of masonry units in a masonry structure is provided. The steps for accomplishing the method include sensing the location of at least one of the plurality of joints between the plurality of masonry units and transmitting joint location data to a computer control system. Next, the computer control system computes a work path based upon the joint location data. In a further step, the computer control system controls the position and operation of at least one work tool such that the work tool moves along the work path to remove mortar from a portion of one of the plurality of joints along the work path. Finally, the dust and debris generated when the work tool removes mortar from a portion of one of the plurality of joints along the work path is contained and removed.