Until now, most of attentions are paid on the calcium-based inorganic material fabrication by such surface-immobilized organic molecular template (Tugulu et al, 2006; Kumar et al, 2010). However, besides calcium mineral, natural system also provides good biomineralization models for other kinds of useful inorganic materials such as silicate, barite, copper, iron and gold. The researches on the fabrication of these non-calcium materials by surface-immobilized organic molecular template have been not extensively investigated (Coffman et al, 2004; Kim et al, 2004 & 2005; Morin et al, 2007). Therefore, our aim is to extend the content of the biomineralization mediated by surface-immobilized organic molecular template from classical calcium to a wide range of inorganic and metal materials through rationally engineering surface molecular template from small functional groups to macromolecules. We for the first time initiated this program in 2005 (Zhang et al, 2005) for the synthesis of silver nanoparticles mediated by surface-immobilized peptides, and after that, a series of researches in this field were reported to exploit the mediation ability of surface-immobilized organic molecule at different molecular scale, including small functional groups for the synthesis of titanium, zinc and silicon oxide films (Yang et al, 2007 and 2008; Gan et al, 2010), oligomer-grade peptides for the synthesis of gold, silver, platinum nanoparticles and superstructures (Zhang et al, 2006 and 2008; Wang et al, 2007; Li et al, 2007) and macromolecular brush for the fabrication of zinc oxide quantum dot and organic/inorganic hybrid nanocomposite film (Zou et al, 2009).In this chapter, we will systematically summarize the data obtained from our group. Engineered surface organic molecular template from our group could be categorized into three levels, depends on the size of surface immobilized molecule on substrates (Figure 1): level (1). small functional groups-mediated inorganic oxide deposition, growth and assembly; level (2). biomolecules such proteins, enzymes and peptides could be immobilized on small functional group-functionalized surface and these surface- immobilized biomolecules (i.e. inorganic-binding peptide) are further used as organic template to mediate noble metal deposition and growth; level (3). macromolecular (polymer) brush-mediated formation of semiconductor quantum dots in polymer matrix to fabricate organic/inorganic hybrid nanocomposites.