We present a light emitting diode (LED)-based optical waveguide array that can optogenetically modulate genetically targeted neurons in the brain. The reusable part of the system consists of control electronics and conventional multi-wavelength LED. The disposable part comprises optical fibers assembled with microlens array fabricated on a silicon die. Both parts can be easily assembled and separated by snap fit structure. Measured light intensity is 3.35 mW/mm(2) at 469 nm and 0.29 mW/mm(2) at 590 nm when the applied current is 80 mA. In all the tested conditions, the light-induced temperature rise is under 0.5 degrees C and over 90% of the relative light intensity is maintained at 2 mm-distance from the fiber tips. We further tested the efficiency of the optical array in vivo at 469 nm. When the optical array delivers light stimulation on to the visual cortex of a mouse expressing channelrhodopsin-2, the neural activity is significantly increased. The light-driven neural activity is successfully transformed into a percept of the mouse, showing significant learning of the task detecting the cortical stimulation. Our results demonstrate that the proposed optical array interfaces well with the neural circuits in vivo and the system is applicable to guide animal behaviors.