Recently, high throughput screening for microorganisms with desired characteristics from a large heterogeneous population has become possible. Single cell separation has taken on increasing significance in recent years, and several different methods have been proposed so far. In this paper, we introduce several cell manipulation methods aiming at single cell separation and investigation. At first, methods for the separation of microorganisms are classified. Then, we introduce two different approaches, that is, (1) indirect manipulation using laser trapped microtools and (2) thermal gelation.