The Jupiter's moon Europa is believed to be one of the few bodies in the Solar System able to host habitable environments. Compelling evidence for the existence of a subsurface ocean was provided by the magnetic field measurements carried out by the Galileo spacecraft.The NASA/JPL Europa Clipper mission is scheduled for launch in the early 2020s. Due to the harsh Jovian radiation environment and budget limitations, the initial concept of an orbiter was abandoned, and the spacecraft will perform only multiple flybys of the moon. Although Clipper will investigate the surface and subsurface properties with a powerful suite of instruments, such approach is not very favourable to a thorough investigation of Europa's deep interior structure.In 2015 the Europa Clipper project announced the possibility to carry an additional flight element with a mass of about 250 kg. We then started investigating a smallest mission aimed at regaining the original science objectives of Clipper for studying the deep interior structure of Europa. Although this additional mass is no longer available, we describe here a mission concept, based on a mothercraft-daughtercraft configuration, which could be of interest to future exploration missions. Our proposal is based on a small spacecraft, the Europa Tomography Probe (ETP), to be inserted in a polar orbit around Europa with a lifetime of a few months. ETP should carry only a magnetometer and a transponder for inter-satellite link, thus not foreseeing any direct link to ground. By exploiting the magnetic induction effect from Jupiter, the magnetometer will measure Europa's magnetic polarizability, thus providing information on the thickness and conductivity of the internal salty ocean, while the ETP transponder will enable a two-way relay link with the mother spacecraft during Europa flybys. The relay link will be used to transfer telemetry data and to carry out range rate measurements on board Clipper. This configuration minimizes the required power on ETP and provides high quality Doppler observables using an ultra-stable oscillator hosted on Clipper. The limiting noise in Doppler measurements will be the frequency stability of ETP and Clipper relay electronics. Doppler data allow the determination of Europa's static gravity field with high resolution along with its variable part due to eccentricity tides (Love number k2). Measurements of the moon's gravity also provide accurate data on its rotational state (e.g., Europa's obliquity and libration amplitude). Furthermore, the inter-satellite Doppler observables can improve the accuracy in the determination of Clipper's position relative to Europa at the level of a few meters in the radial direction. The precise positioning of the main spacecraft relative to Europa and the altimetric measurements from the radar REASON could be exploited to measure the tidal displacement (Love number h2) of the outer icy shell.The NASA's Europa Clipper is viewed as the first applicable study case for the mission concept presented in this paper, which is of general interest to a class of similar flyby missions that can be conceived not only for the Jovian system, but also for Saturn and the ice giants of the solar system, Uranus and Neptune. In the latter case, for example, a small orbiter of Triton could significantly boost the science return from a larger spacecraft focusing on the observation of the planet. In the case of Europa, we show that joint magnetic field, gravity, and possibly altimetric measurements, will place strong constraints on the deep interior structure of the moon and provide a good determination of the ice shell thickness and ocean depth.