Heterogeneous nucleation and crystal growth on protein substrates are critical steps in biological hard tissue formation. Self assembled monolayers can be derivatized with various organic functional groups to mimic the “nucleation proteins” for induction of mineral growth. Studies of nucleation and growth on SAMs can provide a better understanding of biomineralization and can also form the basis of a superior thin film deposition process. We demonstrate that micron-scale, electron and ion beam, lithographic techniques can be used to pattern SAMs with functional organic groups that either inhibit or promote mineral deposition. Patterned films of iron oxyhydroxide were deposited on the areas patterned with nucleation sites. Studies of the deposition kinetic of these films show that the surface indeed induces heterogeneous nucleation and that film formation does not occur via absorption of polymers or colloidal material formed homogeneously in solution. The nucleus interfacial free energy was calculated to be 88 mJ/m2 on a SAM surface composed entirely of sulfonate groups.