High power laser systems, high power laser tools, and methods of using these tools and systems for opening up damaged wells and for cutting, sectioning and removing structures objects, and materials, and in particular, for doing so in difficult to access locations and environments, such as offshore, underwater, or in hazardous environments, such as nuclear and chemical facilities. And, high power laser systems, high power laser tools, and methods of using these systems and tools for providing rock-to-rock plugs for decommissioning of wells.