A real-time, 3D, non-linear microscope measuring system and method for examining a set of microscopic image points in different image planes. The system comprises a pulsed laser or parametric oscillator light source generating an examining optical signal, and is applicable to measure and/or photochemically stimulate pre-selected points within a short time interval. The system further comprises a bundle of fibers composed of optical fibers or other waveguides, a rapidly working optical switch, a imaging system, a light source and an optical system. The examining optical signal is a fluorescent or other optical signal imaged on the required spot.