Previous work (Tull, E. J.; Bartlett, P. N.; Ryan, K. R. Langmuir 2007, 14, 7859; Tull, E. J.; Bartlett, P. N. Colloids Surf., A 2008, 327, 71) has demonstrated that, since convective forces have little influence over spheres in unstable sols, many conventional assembly techniques are ineffective for the organization of glassy spheres > or =5 microm in diameter into sparse patterns of interest for optoelectronic device applications. Carefully designed bifunctional substrates are required for both planar and "in cavity" assembly. In the present work, novel selective chemical modification of structured Ta2O5/glass substrates has been used to generate surfaces tailored to the assembly of glass microspheres from aqueous solution. Uniform arrays of 40-60 microm diameter glass spheres have been produced in pits of half-diameter depth, demonstrating the suitability of this technique for fabricating optical devices where light is coupled from a waveguide into the equator of a sphere. Individual aspects of the assembly process have been examined, and their influence over defect densities and the positioning of the assembled spheres is discussed.