Using a micro particle imaging velocity technique, we resolve for the first time the three dimensionnal structure of wormlike shear banding flows in straight microchannels. The study revealed two effects, which should be generic for shear banding flows: the first is a strong amplification of the confinement induced by the edge of the channel, the second is an instability of the interface between the shear bands. A detailed quantitative comparison of our experimental measurements with a theoretical study of the diffusive Johnson Segalman model leads to excellent agreement. Our study clarifies the nature of shear banding flow instabilities, and shows that, despite the challenging complexity of the situation and the uncertainty regarding their molecular structure, shear banding flows in confined geometries are amenable to quantitative modelling, a feature that opens pathways to their practical utilization.