There is disclosed a new low-level laser therapy apparatus and method of treating tissue. The invention includes a laser system that uses laser diodes and/or alternatively light emitting diodes (LED's), or both, and a digital interface that gives the operator the ability to generate sine waves or scalar waves as opposed to the simple on/off square waves. The invention also enables the operator to modulate not only the frequency, but also other wave characteristics such as the amplitude and phase. In one aspect, the invention involves modulating the phase relationship between multiple waves by taking one channel or wave which is pulsed through the laser system and then running a second channel or wave in relationship to the first channel, thereby creating a phased relationship, which has been discovered to provide a therapeutic and quantum healing effect on tissue. In one exemplary embodiment, the laser system of the invention may have a phase relationship of approximately 180 degrees which provides a beneficial therapeutic and quantum healing effect and, in particular, neutralizes or deletes cellular memory.