A system for preparing and holding specimens for microscopic analysis including a capsule having an open end, an opposite end including at least one aperture and a reservoir. The system also includes an insert with a base including at least one aperture. The insert fits within and engages an inner wall of the reservoir to secure the insert within the reservoir. The system also includes an insertion tool configured to engage the insert. The insertion tool is sized to position the insert within the reservoir at a variety of positions within the reservoir. The insertion tool will disengage the insert once the insert is positioned within the reservoir. A method of positioning a specimen within a capsule for processing the specimen in preparation for microscopic analysis. A tray for holding a plurality of pipette tips in such a way that a lower end of each pipette tip is sealed.