A tray or holder for tissue specimens, especially of excised tissue, such as biopsied specimens, is used with a confocal imaging system. The tray may be disposable after imaging of the specimen carried therein or may archive the specimen. A window supports the specimen. Clamps mounted inside the tray restrain the tissue. A compliant bag is mounted outside the tray on one side of a window of the tray on which the specimen is disposed. During imaging the specimen is immersed in a liquid contained in the tray having an index of refraction which closely matches the index of refraction of the tissue. The bag also contains an index matching liquid preferably having the same index as the liquid in the tray. Selecting an immersion liquid, which equals the refractive index of the near surface tissues, minimizes wavefront distortion which may result from an effectively corrugated surface of the specimen.