A hybrid system consisting of a scanning electrochemical microscope (SECM) and scanning confocal microscope (SCFM) was fabricated and used for micropatterning and imaging of diaphorase immobilized on a glass substrate. Simultaneous imaging of the diaphorase spots demonstrated that the SECM can provide information on a localized enzyme reaction, while the SCFM affords information on the location of the active enzyme. By using this SECM/SCFM system, spatially selective deactivation of diaphorase was performed by inducing a local electrochemical reaction or by irradiating with the focused laser. The resulting patterns of diaphorase were simultaneously imaged with the SECM/SCFM system.