A system and method for fiber optic bundle-based illumination for an imaging system is disclosed. According to one embodiment of the present invention, the system includes a fiber optic bundle that comprising a plurality of optical fibers. Each optical fiber receives light from a light source. The system also includes a beam forming element that selects a mode of operation for the imaging system. The system further includes a beam deflecting device that deflects the light on a sample. According to one embodiment of the present invention, the method includes the steps of (1) selecting a mode of operation for the imaging system; (2) transmitting light from at least one light source through a fiber optic bundle, the fiber optic bundle comprising a plurality of optical fibers; (3) providing a beam forming element based on the selected mode of operation; and (4) deflecting the focused light on a sample.