Lignin applications have exponentially multiplied during the past decade. Most of these applications use Kraft lignin as a starting point in an attempt to valorize this specific byproduct of the Kraft process. However, an even wider range of applications becomes possible if we can obtain less degraded lignins; from fine chemicals production to UV screening, energy storage, antimicrobial products and carbon fibers to name a few. These properties greatly depend on the structure of lignin, which has been proven to be altered during most of the extraction processes hitherto used. Understanding the structure of native lignin will give us the opportunity to finetune extraction protocols to target and preserve the unique native lignin structure. In our projects we developed a sequential, mild and green extraction protocol and were able to characterize most of the lignin contained in our spruce samples (up to 75%), to identify problems in extraction methodologies used until now as classical methods, and to study the effect of ball milling, a popular mechanical pretreatment, on the structure of lignin. A re-optimization of the protocol has been performed to be able to study lignin in hardwoods, since the lignin building blocks, or monolignols, differ between softwoods and hardwoods, and the woods have different material properties that affect extraction processes. We hope the results of these studies will help the development of a lignin-first biorefinery, exploring the full potential of lignin, the second most abundant biopolymer on Earth.