During embryogenesis, complex balances of growth factors (GFs) influence differentiation into the three germ layers: endoderm, mesoderm, and ectoderm. Current models of development are limited to introduction of soluble factors without the ability to localize GFs to specific layers within a 3D cell scaffold. FGF2 was recruited to its cell surface receptor by glycosaminoglycan (GAG) mimetics to direct stem cell differentiation into neural rosettes. This provided the basis for testing the incorporation of these GAG mimetics into a three-dimensional (3D) scaffold, more representative of a developing embryo or organoid. Altering the structure of the GAG mimetics affected their penetration into the EBs. The longer the GAG mimetic, the larger the molecular weight and size thus taking longer to incorporate into the EB compared to a shorter GAG. No correlations were observed between the ability to penetrate EBs and the different charges of the sugars ligated to the GAG mimetics. The short GAG mimetic recruited FGF2 throughout the EBs showing their ability to localize GFs in a 3D cell scaffold. Future directions include patterning Erk phosphorylation, the first step in the signaling cascade leading to Neuroectoderm differentiation, to the localization of FGF2 by the GAG mimetics. Overall these GAG mimetics show promise as tools to further explore stem cell differentiation through the recruitment of growth factors in three dimensional cell models.