Bulk ceramics including alumina, zirconia, and silicon nitride ceramics are manufactured through a multi-stage and continuous process from raw powders to shaping and sintering. So far, we have developed a three-dimensional (3D) observation methods for various powder compacts, and examine the effects on subsequent processes. 3D observation has much more information than cross-sectional observation and is suitable for structural evaluation. In this study, we investigated the causes of large defects in ceramics using semi-transparent images using the optical and the near-infrared microscopy of thin samples and using the micro-computed tomography. Observation objects were powder compacts, compacts after binder burnouted, and sintered ceramics. Shaping methods are dry-pressing, slip-casting, tape-casting, and extrusion molding. In the dry pressing method of alumina and zirconia, the microstructure of the compact was derived from the properties of the granules (organic matter, shape and density of granules). After binder burnout, the defect was slightly opened. During sintering, the defects became invisible, but at the final stage of sintering, the defects opened up and became larger. In slip casting and tape casting, agglomerates had also effects, and in extrusion, the organic matter contained in the compound during molding caused the formation of defects. Thus, 3D observation provides useful information for improving various molding methods.