This paper proposes a capture device to manipulate and transport a cellular aggregate in a micro-well. A cellular aggregate (a few hundreds μm in diameter) is currently manipulated by a pipette. The manual manipulation by a pipette has problems; low reliability, low throughput, and difficulty in confirmation of task completion. We took into account of compatibility with existing methods such as a micro-well-plate and designed for the capture device of a cellular aggregate in a micro-well. A newly developed capture device flows and carries a cellular aggregate from a bottom of a well to a trap of the capture device. We designed a curved surface at the bottom of the capture device to form a space to act as a channel between the inner wall of the micro-well. This paper presents concept, design, fabrication, and of the proposed cellular aggregate capture, followed by successful experimental results.