Laser-based methods and systems for removing one or more target link structures of a circuit fabricated on a substrate includes generating a pulsed laser output at a predetermined wavelength less than an absorption edge of the substrate are provided. The laser output includes at least one pulse having a pulse duration in the range of about 10 picoseconds to less than 1 nanosecond, the pulse duration being within a thermal laser processing range. The method also includes delivering and focusing the laser output onto the target link structure. The focused laser output has sufficient power density at a location within the target link structure to reduce the reflectivity of the target link structure and efficiently couple the focused laser output into the target link structure to remove the target link structure without damaging the substrate.