There are many factors that have the potential to limit significant advances in device technology. These include the ability to arrange materials at shrinking dimensions and the ability to successfully integrate new materials with better properties or new functionalities. To overcome these limitations, the development of advanced processing methods that can organize various combinations of materials at nano-scale dimensions with the necessary quality and reliability is required. We have explored using a gallium focused ion beam (FIB) as a method of integrating highly mismatched materials with silicon by creating template patterns directly on Si with nanoscale resolution. These templates are potentially useful as a means of locally controlling topography at nanoscale dimensions or as a means of locally implanting Ga at specific surface sites. We have annealed these templates in vacuum to study the effects of ion dosage on local Ga concentration and topography. We have also investigated the feasibility of creating Ga nanodots using this method that could eventually be converted to GaN through a nitridation process. Atomic force microscopy and electron microscopy characterization of the resulting structures are shown for a variety of patterning and processing conditions.