The magnetic structure of the in-plane skyrmions in epitaxial MnSi/Si(111) thin films is probed in three dimensions by the combination of polarized neutron reflectometry (PNR) and small angle neutron scattering (SANS). We demonstrate that skyrmions exist in a region of the phase diagram above at temperature of 10 K. PNR shows the skyrmions are confined to the middle of the film due to the potential well formed by the surface twists. However, SANS shows that there is considerable disorder within the plane indicating that the magnetic structure is a 2D skyrmion glass.