There are two types of apertures, hexagonal and circular, to fabricate planar GRIN microlens arrays with hexagonal aperture and high fill factor by ion-exchange and photolithography. By the designed photomasks of hexagonal and circular aperture, ion-exchange, photolithography and time sampling, the characteristics of ion-diffusion during fabricating the two types of planar GRIN microlens arrays with high fill factor are tested and analyzed. Then we obtain the features of ion-diffusion in such two types of apertures, which are helpful to fabricate planar GRIN microlens arrays with high fill factor when the aperture size and aperture spacing are given.