A key feature in the understanding of the mechanisms of integration of implant materials is a deepened in-sight of the elemental and molecular composition of the interface zone between the implant and tissue. To analyze the interface at the ultrastructural level, transmission electron microscopy (TEM) is needed. However, techniques to fabricate thin foils for TEM are difficult and time consuming. By using focused ion beam microscopy (FIB) for site-specific preparation of TEM-samples, intact interfaces between bioceramics and calcified tissue can be prepared. The site-specific accuracy of the technique is about 1 mm. By using a dual-beam FIB, which is a combined scanning electron and focused ion beam microscope, the sample can be imaged with both electrons and ions (generating both secondary electrons and ions). Results from interface studies between Ca-aluminate based orthopaedic cement, dental materials, HA-coated Ti-implants and bone are presented. The interfaces were imaged in scanning-TEM and bright field mode, the crystal structures were determined using electron diffraction and elemental composition analyzed with energy dispersive spectroscopy. The technique fulfils a demand to correlate the surface properties of bioceramic implants with the structure and composition of preserved interfaces with tissues.