A method and system for fusing a region in the spine involve the use of at least one guide tube to pass instruments and substances into the spinal region in a minimally invasive manner. In the preferred practice of the method, a guide tube is anchored to a vertebra and the guide tube is moved to thereby position the vertebra. A steerable drilling tool is passed through the guide tube and steered into position to abrade at least a portion of an intervertebral disc and thereby create a cavity in the disc. A flowable substance is passed into the cavity and permitted to solidify to establish fusion in the cavity. Optionally, an uninflated balloon is inserted into the cavity and the balloon is filled with the flowable substance to contain the flowable substance.