We study the microstructure of a granular amorphous silica ceramic material synthesized by spark plasma sintering. Using monodisperse spherical silica particles as precursor, spark plasma sintering yields a dense granular material with distinct granule boundaries. We use selective etching to obtain nanoscopic pores along the granule borders. We interrogate this highly interesting material structure by combining scanning electron microscopy, X-ray computed nanotomography and simulations based on random close packed spherical particles. We determine the degree of anisotropy caused by the uni-axial force applied during sintering, and our analysis shows that our synthesis method provides a means to avoid significant granule growth and to fabricate a material with well-controlled microstructure.