There are several ways to remove the inner portion of the disc. The procedure is called a nucleoplasty. Using heat to destroy the tissue is a commonly used method. None of these methods of surgical decompression actually removes the tissue exactly behind the protrusion.
Part of the reason for the lack of precision is the difficulty of getting to the inner portion of the disc. The neurosurgeon can use an anterior (from the front of the spine) or posterior (from the back of the spine) approach. But with either technique, it’s important to avoid damaging nearby soft tissue structures.
The surgeon doesn’t always remove nuclear material within the protrusion. This only happens when the protrusion is right along the path used to access the disc. Getting to the exact area of protrusions may be possible in the future with more advanced technology.
Studies show that just reducing the volume of the inner disc is enough to alter tension in the outer covering of the disc. The overall result may be to reduce tension on the spinal nerve root. Removing the source of inflammation can have the effect of reducing painful symptoms. You have probably benefitted from this indirect effect of nucleoplasty.