We describe a technological platform developed for miniaturization of optical imaging instruments, such as laser scanning confocal microscopes or Optical Coherence Tomography devices. The platform employs multi-wafer vertical integration approach, combined with integrated glass-based micro-optics and heterogeneous bonding and interconnecting technologies. In this paper we focus on the unconventional fabrication methods of monolithic micro-optical structures and components in borosilicate glass (e.g. micro beamsplitters, refractive microlenses) for optical beam shaping and routing. In addition, we present hybrid laser-assisted integration of glass ball microlenses on the silicon MEMS actuators for transmissive beam scanning as well as methods of electrical signals distribution through thick glass substrates, based on HF etched via holes.