Methods and apparatus for UAV-enabled marking of surfaces during manufacture, inspection, or repair of limited-access structures and objects. A UAV is equipped with a marking module that is configured to apply marking patterns (e.g., alignment features) of known dimensions to surfaces. The marking module may include a 2-D plotter that enables free-form drawing capability. The marking process may involve depositing material on the surface. The marking material may be either permanent or removable. A “clean-up” module may be attached to the UAV platform instead of the marking module, and may include solvents and oscillating or vibrating pads to remove the marks via scrubbing. The clean-up module can also be used for initial surface preparation.