Due to their extraordinary physical and chemical properties carbon nanotubes reveal promising potential as biomedical agents for heating, temperature sensoring and drug delivery on the cellular level. Filling carbon nanotubes with tailored materials realises nanoscaled containers in which the active content is encapsulated by a protecting carbon shell. We describe different synthesis routes and show the structural and magnetic properties of carbon nanotubes. In particular, the filling with magnetic materials offers the potential for hyperthermia applications while the insertion of NMR active substances allows the usage as markers and sensors. The potential of carbon nanotubes for biomedical applications is highlighted by hyperthermia studies which prove their applicability for local in situ heating. In addition we have shown that a non-invasive temperature control by virtue of a carbon-wrapped nanoscaled thermometer and filling with anti-cancer drugs is possible.