Autocloned photonic crystals have corrugated multilayer structure. By related process technology, we can easily fabricate an array of polarizers or waveplates. Patterned photonic crystals are versatile component of many optical systems. This paper focuses on their use in optical microscopy. The main topics are: 1. Use of polarization imaging in microscopy, 2. generation of radial/circular polarization by a polarizer having concentric corrugations, 3. a "longitudinal polarization slit" (a new component) and its function in confocal microscopy, and 4. a polarization converter for generating "z-polarized" light at the focal point. In every application above, autocloned photonic crystals play a central role.