BACKGROUND In combination with magnetoencephalographic (MEG) data, accurate knowledge of the brain’s structure and location provide a principled way of reconstructing neural activity with high temporal resolution. However, measuring the brain’s location is compromised by head movement during scanning, and by fiducial-based co-registration with magnetic resonance imaging (MRI) data. The uncertainty from these two factors introduces errors into the forward model and limit the spatial resolution of the data. NEW METHOD We present a method for stabilizing and reliably repositioning the head during scanning, and for co-registering MRI and MEG data with low error. RESULTS Using this new flexible and comfortable subject-specific head-cast prototype, we find within-session movements of { extless}0.25mm and between-session repositioning errors around 1mm. COMPARISON WITH EXISTING METHOD(S) This method is an improvement over existing methods for stabilizing the head or correcting for location shifts on- or off-line, which still introduce approximately 5mm of uncertainty at best (Adjamian et al., 2004; Stolk et al., 2013; Whalen et al., 2008). Further, the head-cast design presented here is more comfortable, safer, and easier to use than the earlier 3D printed prototype, and give slightly lower co-registration errors (Troebinger et al., 2014b). CONCLUSIONS We provide an empirical example of how these head-casts impact on source level reproducibility. Employment of the individual flexible head-casts for MEG recordings provide a reliable method of safely stabilizing the head during MEG recordings, and for co-registering MRI anatomical images to MEG functional data.