A sample encapsulation system includes a fixture, a base, a chamber having an inlet and a chamber housing. The housing has inner and outer housings. The chamber is mounted in the inner housing. The base, chamber and housing are affixed to one another and movable in the fixture. A cap has a first ram operably mounted thereto for engaging the chamber inlet. A second ram in the chamber opposite the inlet moves toward and away from the first ram. A heating assembly is positioned in the inner housing and a cooling assembly including a cooling jacket defined in part by the inner and outer housings includes a manifold. The chamber, housing and base are movable toward and away from the cap for engaging and disengaging the first ram with the chamber during and after the encapsulation cycle, respectively. The cooling system includes a vacuum breaker to self-drain following cooling.