Thin films of 3-aminopropyltriethoxysilane (APTES) are commonly used to promote adhesion between silica substrates and organic or metallic materials with applications ranging from advanced composites to biomolecular lab-on-a-chip. Unfortunately, there is confusion as to which reaction conditions will result in consistently aminated surfaces. A wide range of conflicting experimental methods are used with researchers often assuming the creation of smooth self-assembled monolayers. A range of film morphologies based on the film deposition conditions are presented here to establish an optimized method of APTES film formation. The effect of reaction temperature, solution concentration, and reaction time on the structure and morphology was studied for the system of APTES on silica. Three basic morphologies were observed: smooth thin film, smooth thick film, and roughened thick film.