Ion beam therapy is a rapidly developing method for treatment of certain types of cancer. A main advantage of ions is that they deposit most of the energy at the end of their range according to the Bragg curve. Unfortunately, the ion beam often generates a substantial amount of energetic secondary particles with not negligible range. Thus, a fraction of the dose is deposited by other than the primary ions outside of the planned volume. It is, therefore, important to estimate and experimentally verify the distributions of these secondary particles. It is particularly difficult to identify fast neutrons generated by ions in tissue. Fast neutrons are usually detected via their interaction (scattering) with hydrogen nuclei (proton). The proton recoiled by the scattered neutron is subsequently detected by a suitable sensor. The problem is that certain fraction of secondary particles consists of protons as well. Therefore, it is necessary to distinguish protons recoiled by neutrons from protons naturally present in the sample. In this work we present the experimental technique enabling the separation of fast neutrons from protons. The technique uses a 3D sensitive voxel detector composed of several layers of Timepix pixel detectors. These layers are interlaced with a hydrogen rich material (plastic) serving as a convertor of neutrons to recoiled protons. The device records the traces of all interacting radiation providing the time stamp and/or deposited energy for each single particle. A proton passing through the detector creates a trace in all layers, whereas a protons recoiled by neutron originates in the convertor inside of the structure creating a trace in the inner layers only. This way it is possible to distinguish the protons from neutrons with very high selectivity. The technique can be easily extended for detection of slow neutrons. An initial experimental study to register the outcoming neutron radiation was performed at the Heidelberg Ion Beam Therapy Center (HIT) in Germany using medical proton and carbon ion beams. This work is carried out in frame of the Medipix Collaboration.